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/7930160/working' mkdir: created directory `/scratch/stefan/7930160/working/protonate' Storing results in /scratch/stefan/7930160/finished Working in /scratch/stefan/7930160/working /scratch/stefan/7930160/working /scratch/stefan/7930160 /scratch/stefan/7930160/working/protonate /scratch/stefan/7930160/working /scratch/stefan/7930160 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' Jan 20, 2020 8:22:54 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:23:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:24:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:24:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:24:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:24:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:25:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:25:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:25:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:25:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:25:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:26:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:26:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:26:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:26:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:27:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:27:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:27:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 20, 2020 8:28:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1122 protomers created Coalesing and merging protomers 1074 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1086 protomers after new stereo-center expansion /scratch/stefan/7930160/working /scratch/stefan/7930160 Bulk generating 3D conformations all protomers in /scratch/stefan/7930160/working/3D mkdir: created directory `/scratch/stefan/7930160/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7930160/working/protonate/xaaaade-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' 1087 3D conformations generated for 1000 compounds Building REAL300000082001 mkdir: created directory `/scratch/stefan/7930160/working/building' mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082001' /scratch/stefan/7930160/working/building/REAL300000082001 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082001 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082001/0 /scratch/stefan/7930160/working/building/REAL300000082001 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1 `/scratch/stefan/7930160/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2COC3=CC=C(F)C=C32)=CC=C1F) `REAL300000082001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082001 none O=C([O-])C1=CC(NN=C2COC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 40, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 9, 1, 1, 1, 1, 1, 39, 39] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082001 none O=C([O-])C1=CC(NN=C2COC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 37, 1, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 1, 1] 40 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082001 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082001 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `/scratch/stefan/7930160/finished' Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082001/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082001 Building REAL300000082002 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082002' /scratch/stefan/7930160/working/building/REAL300000082002 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082002 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082002/0 /scratch/stefan/7930160/working/building/REAL300000082002 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/2 `/scratch/stefan/7930160/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082002 none CC(CCC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 8, 63, 141, 175, 201, 201, 175, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 150, 150, 175, 170, 201, 201, 201, 201, 1, 1, 1] 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]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082002 none CC(CCC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 23, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 22, 23, 23, 23, 5, 5, 3, 3, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082002 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082002 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082002/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082002 Building REAL300000082003 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082003' /scratch/stefan/7930160/working/building/REAL300000082003 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082003 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082003/0 /scratch/stefan/7930160/working/building/REAL300000082003 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/3 `/scratch/stefan/7930160/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C3=CC=CS3)=C2)=CC=C1F) `REAL300000082003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082003 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C3=CC=CS3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 82, 117, 82, 82, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 82, 82, 81, 81, 82, 39, 6, 1, 1, 13, 13, 13, 1, 82, 82] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 15, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082003 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C3=CC=CS3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 30, 30, 82, 82, 82, 82, 82, 82, 201, 201, 201, 201, 82, 1, 1, 1, 1, 1, 7, 30, 82, 82, 201, 201, 201, 82, 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: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082003 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C3=CC=CS3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 149, 54, 54, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 149, 54, 13, 13, 1, 1, 1, 13, 201, 201] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082003 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082003 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082003/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082003 Building REAL300000082004 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082004' /scratch/stefan/7930160/working/building/REAL300000082004 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082004 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082004/0 /scratch/stefan/7930160/working/building/REAL300000082004 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/4 `/scratch/stefan/7930160/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)N(C)C)=C1) `REAL300000082004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082004 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 25, 41, 41, 41, 41, 41, 41, 48, 48, 41, 1, 1, 1, 1, 1, 1, 6, 20, 63, 63, 63, 64, 1, 11, 11, 11, 25, 41, 41, 41, 1, 1, 1, 20, 20, 64, 64, 64, 64, 64, 64, 1] 201 rigid atoms, others: [1, 34, 35, 36, 45, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 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: 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: REAL300000082004 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 15, 41, 41, 41, 41, 41, 84, 131, 201, 201, 201, 201, 41, 15, 15, 15, 5, 1, 1, 1, 41, 41, 41, 131, 131, 201, 201, 201, 201, 201, 201, 41] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 603 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082004 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082004 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082004/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082004 Building REAL300000082005 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082005' /scratch/stefan/7930160/working/building/REAL300000082005 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082005 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082005/0 /scratch/stefan/7930160/working/building/REAL300000082005 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/5 `/scratch/stefan/7930160/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CCC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1) `REAL300000082005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082005 none CC1=CC(CCC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 97, 45, 9, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 175, 201, 201, 201, 201, 109, 105, 102, 102, 45, 45, 45, 45, 1, 1, 1, 201, 201, 181] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082005 none CC1=CC(CCC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 9, 26, 26, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 7, 7, 9, 9, 26, 26, 26, 26, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 40, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082005 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082005 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082005/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082005 Building REAL300000082006 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082006' /scratch/stefan/7930160/working/building/REAL300000082006 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082006 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082006/0 /scratch/stefan/7930160/working/building/REAL300000082006 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/6 `/scratch/stefan/7930160/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=CC=C1F) `REAL300000082006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082006 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 93, 93, 93, 93, 93, 34, 7, 1, 1, 1, 1, 1, 1, 93, 93] 93 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 35, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082006 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 12, 65, 65, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 12, 65, 93, 93, 93, 93, 93, 93, 1, 1] 93 rigid atoms, others: [1, 3, 4, 5, 6, 35, 25, 22, 23, 24, 36, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082006 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082006 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082006/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082006 Building REAL300000082007 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082007' /scratch/stefan/7930160/working/building/REAL300000082007 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082007 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082007/0 /scratch/stefan/7930160/working/building/REAL300000082007 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/7 `/scratch/stefan/7930160/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2OC2CCCC2)=CC=C1F) `REAL300000082007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082007 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 68, 101, 68, 68, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 68, 68, 68, 68, 68, 32, 9, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 68, 68] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 315 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: REAL300000082007 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 9, 30, 30, 68, 68, 68, 68, 68, 68, 159, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 30, 68, 68, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 407 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082007 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 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, 52, 52, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 52, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 465 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082007 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082007 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082007/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082007 Building REAL300000082008 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082008' /scratch/stefan/7930160/working/building/REAL300000082008 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082008 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082008/0 /scratch/stefan/7930160/working/building/REAL300000082008 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/8 `/scratch/stefan/7930160/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(C3=CSC=C3)=N2)=CC=C1F) `REAL300000082008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082008 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CSC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [118, 105, 118, 105, 105, 40, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 105, 105, 105, 105, 105, 40, 8, 1, 4, 4, 4, 105, 105] 166 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082008 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CSC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 63, 63, 105, 105, 105, 105, 166, 166, 166, 166, 105, 1, 1, 1, 1, 1, 11, 63, 105, 166, 166, 166, 1, 1] 166 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082008 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CSC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 166, 91, 25, 25, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 166, 166, 166, 166, 166, 90, 25, 4, 1, 1, 1, 166, 166] 166 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 329 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082008 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082008 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082008/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082008 Building REAL300000082009 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082009' /scratch/stefan/7930160/working/building/REAL300000082009 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082009 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082009/0 /scratch/stefan/7930160/working/building/REAL300000082009 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/9 `/scratch/stefan/7930160/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OCC2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CS2)C=C1) `REAL300000082009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082009 none CC1=CC=C(OCC2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 8, 8, 35, 69, 69, 69, 69, 69, 69, 103, 103, 69, 1, 1, 21, 21, 21, 21, 21, 21, 21, 9, 9, 8, 35, 69, 69, 69, 1, 21, 21] 201 rigid atoms, others: [6, 7, 8, 9, 10, 39, 23, 24] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 310 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: REAL300000082009 none CC1=CC=C(OCC2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 22, 22, 22, 51, 51, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 22, 22, 1, 1, 2, 2, 2, 1, 1, 6, 6, 51, 138, 201, 201, 201, 22, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 436 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082009 none CC1=CC=C(OCC2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 189, 69, 69, 69, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 189, 189, 39, 9, 1, 1, 1, 69, 201, 201] 201 rigid atoms, others: [36, 37, 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, 35, 39, 40, 41]) total number of confs: 605 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082009 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082009 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082009/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082009 Building REAL300000082010 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082010' /scratch/stefan/7930160/working/building/REAL300000082010 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082010 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082010/0 /scratch/stefan/7930160/working/building/REAL300000082010 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/10 `/scratch/stefan/7930160/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082010 none C#CCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 114, 93, 40, 40, 54, 54, 23, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 201, 201, 201, 112, 113, 54, 53, 22, 6, 1, 1, 1, 54, 54] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 754 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: REAL300000082010 none C#CCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [21, 21, 9, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 53, 53, 53, 53, 53, 54, 85, 85, 53, 1, 1, 21, 20, 20, 9, 9, 1, 1, 6, 26, 53, 53, 53, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 36, 29, 30, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 313 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082010 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082010 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082010/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082010 Building REAL300000082011 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082011' /scratch/stefan/7930160/working/building/REAL300000082011 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082011 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082011/0 /scratch/stefan/7930160/working/building/REAL300000082011 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/11 `/scratch/stefan/7930160/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082011 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 27, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 49 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: REAL300000082011 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 27, 27, 27, 1, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 17, 18, 19, 20, 21, 22, 36, 37, 29, 30, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 50 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082011 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082011 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082011/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082011 Building REAL300000082012 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082012' /scratch/stefan/7930160/working/building/REAL300000082012 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082012 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082012/0 /scratch/stefan/7930160/working/building/REAL300000082012 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/12 `/scratch/stefan/7930160/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082012 none CC(C)(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 112, 158, 158, 112, 112, 112, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 112, 158, 158, 158, 158, 158, 158, 158, 158, 158, 112, 59, 13, 1, 1, 1] 158 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 419 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082012 none CC(C)(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 48, 112, 112, 112, 112, 112, 112, 135, 135, 112, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 47, 112, 112, 112] 158 rigid atoms, others: [1, 4, 5, 6, 7, 8, 21, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082012 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082012 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082012/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082012 Building REAL300000082013 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082013' /scratch/stefan/7930160/working/building/REAL300000082013 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082013 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082013/0 /scratch/stefan/7930160/working/building/REAL300000082013 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/13 `/scratch/stefan/7930160/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F) `REAL300000082013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082013 none O=C([O-])C1=CC(N=NCC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 76, 76, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082013 none O=C([O-])C1=CC(N=NCC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 43, 44, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082013 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082013/1 /scratch/stefan/7930160/working/building/REAL300000082013 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/14 `/scratch/stefan/7930160/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F) `REAL300000082013.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082013 none O=C([O-])C1=CC(NN=CC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 29, 7, 1, 1, 1, 1, 59, 59] 59 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000082013 none O=C([O-])C1=CC(NN=CC2=CN3C=C(Cl)C=CC3=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 48, 48, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 11, 48, 59, 59, 59, 59, 1, 1] 59 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082013 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082013 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082013/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082013/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082013 Building REAL300000082014 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082014' /scratch/stefan/7930160/working/building/REAL300000082014 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082014 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082014/0 /scratch/stefan/7930160/working/building/REAL300000082014 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/15 `/scratch/stefan/7930160/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082014 none CC(C)C1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 47, 78, 47, 47, 47, 47, 47, 47, 46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 78, 78, 78, 78, 78, 78, 78, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 47] 78 rigid atoms, others: [39, 40, 41, 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, 35, 36, 37, 38, 42]) total number of confs: 259 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: REAL300000082014 none CC(C)C1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 46, 46, 47, 47, 76, 76, 47, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 1] 78 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 12, 11, 35, 23, 24, 36, 42, 37] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41]) total number of confs: 199 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082014 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082014 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082014/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082014 Building REAL300000082015 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082015' /scratch/stefan/7930160/working/building/REAL300000082015 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082015 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082015/0 /scratch/stefan/7930160/working/building/REAL300000082015 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/16 `/scratch/stefan/7930160/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082015 none CC1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 1, 1, 1] 38 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 69 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: REAL300000082015 none CC1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 37, 37, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082015 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082015 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082015/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082015 Building REAL300000082016 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082016' /scratch/stefan/7930160/working/building/REAL300000082016 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082016 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082016/0 /scratch/stefan/7930160/working/building/REAL300000082016 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/17 `/scratch/stefan/7930160/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C2C(=C1)OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082016 none CC1=CC(C)=C2C(=C1)OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 1, 1, 1] 43 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 71 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: REAL300000082016 none CC1=CC(C)=C2C(=C1)OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 13, 35, 32, 33, 27, 31] set([36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 73 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082016 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082016 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082016/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082016 Building REAL300000082017 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082017' /scratch/stefan/7930160/working/building/REAL300000082017 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082017 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082017/0 /scratch/stefan/7930160/working/building/REAL300000082017 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/18 `/scratch/stefan/7930160/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(F)C=C23)=CC=C1F) `REAL300000082017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082017 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 10, 1, 1, 1, 1, 1, 1, 43, 43] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 63 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: REAL300000082017 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 10, 43, 43, 43, 43, 43, 43, 1, 1] 43 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082017 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082017 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082017/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082017 Building REAL300000082018 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082018' /scratch/stefan/7930160/working/building/REAL300000082018 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082018 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082018/0 /scratch/stefan/7930160/working/building/REAL300000082018 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/19 `/scratch/stefan/7930160/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082018 none CC1=CC=C(C)C2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1] 46 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 72 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: REAL300000082018 none CC1=CC=C(C)C2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 46, 46, 46] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 13, 35, 32, 33, 27, 28] set([36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082018 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082018 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082018/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082018 Building REAL300000082019 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082019' /scratch/stefan/7930160/working/building/REAL300000082019 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082019 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082019/0 /scratch/stefan/7930160/working/building/REAL300000082019 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/20 `/scratch/stefan/7930160/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082019 none CC1=CC(Br)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 39, 39, 39, 38, 38, 38, 38, 38, 10, 1, 1, 1, 38] 39 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 70 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: REAL300000082019 none CC1=CC(Br)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 38, 38, 38, 39, 39, 38, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 38, 38, 38, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 36, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 66 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082019 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082019 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082019/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082019 Building REAL300000082020 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082020' /scratch/stefan/7930160/working/building/REAL300000082020 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082020 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082020/0 /scratch/stefan/7930160/working/building/REAL300000082020 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/21 `/scratch/stefan/7930160/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082020 none CCCOC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 120, 40, 40, 40, 40, 40, 40, 40, 39, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 201, 201, 201, 201, 201, 144, 144, 40, 40, 40, 40, 40, 40, 8, 1, 1, 1, 40] 201 rigid atoms, others: [40, 41, 42, 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, 38, 39, 43]) total number of confs: 652 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082020 none CCCOC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 39, 39, 40, 40, 70, 70, 40, 1, 1, 28, 28, 28, 28, 28, 15, 15, 1, 1, 1, 1, 1, 1, 8, 40, 40, 40, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 43, 35, 24, 25, 38, 37, 36] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 293 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082020 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082020 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082020/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082020 Building REAL300000082021 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082021' /scratch/stefan/7930160/working/building/REAL300000082021 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082021 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082021/0 /scratch/stefan/7930160/working/building/REAL300000082021 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/22 `/scratch/stefan/7930160/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082021 none CC1=CC(C)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 1, 1, 1, 37] 37 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 61 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: REAL300000082021 none CC1=CC(C)=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 9, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 32, 22, 23, 39, 33, 27, 31] set([35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30]) total number of confs: 67 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082021 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082021 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082021/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082021 Building REAL300000082022 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082022' /scratch/stefan/7930160/working/building/REAL300000082022 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082022 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082022/0 /scratch/stefan/7930160/working/building/REAL300000082022 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/23 `/scratch/stefan/7930160/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(Br)C=CC=C23)=CC=C1F) `REAL300000082022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082022 none O=C([O-])C1=CC(NN=C2CCOC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 54 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: REAL300000082022 none O=C([O-])C1=CC(NN=C2CCOC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082022 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082022 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082022/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082022 Building REAL300000082023 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082023' /scratch/stefan/7930160/working/building/REAL300000082023 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082023 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082023/0 /scratch/stefan/7930160/working/building/REAL300000082023 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/24 `/scratch/stefan/7930160/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCSC3=CC=C(Br)C=C32)=CC=C1F) `REAL300000082023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082023 none O=C([O-])C1=CC(NN=C2CCSC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 56 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: REAL300000082023 none O=C([O-])C1=CC(NN=C2CCSC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 11, 38, 38, 38, 38, 38, 38, 38, 1, 1] 38 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082023 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082023 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082023/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082023 Building REAL300000082024 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082024' /scratch/stefan/7930160/working/building/REAL300000082024 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082024 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082024/0 /scratch/stefan/7930160/working/building/REAL300000082024 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/25 `/scratch/stefan/7930160/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(C3CC3)=N2)=CC=C1F) `REAL300000082024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082024 none O=C([O-])C1=CC(NN=CC2=CSC(C3CC3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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, 8, 8, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [112, 84, 112, 84, 84, 33, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 1, 84, 84, 84, 84, 84, 33, 7, 1, 12, 12, 12, 12, 12, 84, 84] 170 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000082024 none O=C([O-])C1=CC(NN=CC2=CSC(C3CC3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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, 8, 8, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 55, 55, 84, 84, 84, 84, 170, 170, 84, 1, 1, 1, 1, 1, 10, 55, 84, 170, 170, 170, 170, 170, 1, 1] 170 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082024 none O=C([O-])C1=CC(NN=CC2=CSC(C3CC3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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, 8, 8, 1, 1, 1, 14, 1, 5, 5, 5, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 170, 110, 33, 33, 12, 12, 12, 12, 1, 1, 1, 1, 12, 170, 170, 170, 170, 170, 110, 33, 12, 1, 1, 1, 1, 1, 170, 170] 170 rigid atoms, others: [12, 13, 14, 15, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082024 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082024 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082024/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082024 Building REAL300000082025 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082025' /scratch/stefan/7930160/working/building/REAL300000082025 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082025 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082025/0 /scratch/stefan/7930160/working/building/REAL300000082025 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/26 `/scratch/stefan/7930160/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC(F)(F)F)C=C1) `REAL300000082025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082025 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 78, 78, 78, 78, 78, 78, 106, 106, 78, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 1, 1, 6, 6, 6, 31, 78, 78, 78, 1, 1, 16, 16, 1, 1] 201 rigid atoms, others: [1, 34, 37, 38, 33, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 304 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: REAL300000082025 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 78, 78, 51, 78, 185, 201, 201, 201, 201, 78, 78, 31, 31, 31, 8, 1, 1, 1, 78, 78, 201, 201, 78, 78] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 519 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082025 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082025 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082025/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082025 Building REAL300000082026 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082026' /scratch/stefan/7930160/working/building/REAL300000082026 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082026 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082026/0 /scratch/stefan/7930160/working/building/REAL300000082026 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/27 `/scratch/stefan/7930160/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=CC=C1F) `REAL300000082026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082026 none O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 31, 46, 31, 31, 18, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 42, 42, 31, 31, 31, 31, 31, 18, 6, 1, 1, 1, 42, 31, 31] 113 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082026 none O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 4, 18, 18, 31, 31, 31, 31, 31, 18, 31, 31, 31, 79, 113, 113, 1, 1, 1, 1, 1, 4, 18, 31, 31, 31, 113, 1, 1] 113 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082026 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082026 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082026/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082026 Building REAL300000082027 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082027' /scratch/stefan/7930160/working/building/REAL300000082027 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082027 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082027/0 /scratch/stefan/7930160/working/building/REAL300000082027 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/28 `/scratch/stefan/7930160/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1) `REAL300000082027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082027 none CC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 22, 54, 54, 54, 54, 54, 54, 61, 61, 54, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 6, 22, 54, 54, 54, 6, 6] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000082027 none CC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 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, 6, 6, 6, 6, 36, 36, 85, 104, 104, 104, 104, 104, 104, 104, 104, 104, 6, 1, 1, 2, 2, 2, 1, 1, 6, 6, 36, 85, 104, 104, 104, 1, 1] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082027 none CC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [54, 54, 103, 103, 54, 54, 54, 54, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 103, 103, 103, 103, 103, 103, 103, 54, 54, 34, 10, 1, 1, 1, 103, 103] 103 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082027 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082027 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082027/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082027 Building REAL300000082028 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082028' /scratch/stefan/7930160/working/building/REAL300000082028 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082028 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082028/0 /scratch/stefan/7930160/working/building/REAL300000082028 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/29 `/scratch/stefan/7930160/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC[NH+](C)C)=C1) `REAL300000082028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082028 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 1, 1, 1, 1, 1, 1, 4, 12, 14, 16, 16, 16, 1, 4, 4, 4, 8, 8, 8, 8, 1, 1, 1, 12, 12, 14, 14, 16, 16, 16, 16, 16, 16, 1] 22 rigid atoms, others: [1, 34, 35, 36, 14, 15, 16, 17, 18, 19, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 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: REAL300000082028 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OCC[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 6, 8, 8, 8, 8, 8, 12, 21, 21, 22, 22, 22, 8, 6, 6, 6, 2, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 8] 22 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082028 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082028 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082028/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082028 Building REAL300000082029 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082029' /scratch/stefan/7930160/working/building/REAL300000082029 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082029 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082029/0 /scratch/stefan/7930160/working/building/REAL300000082029 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/30 `/scratch/stefan/7930160/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CO2)=CC=C1F) `REAL300000082029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082029 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', '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, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 41, 7, 1, 1, 67, 67] 67 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 24, 25]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082029 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', '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, 8, 8, 1, 1, 1, 1, 17, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 47, 47, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 13, 47, 67, 67, 1, 1] 67 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082029 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082029 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082029/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082029 Building REAL300000082030 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082030' /scratch/stefan/7930160/working/building/REAL300000082030 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082030 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082030/0 /scratch/stefan/7930160/working/building/REAL300000082030 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/31 `/scratch/stefan/7930160/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(CN2CCOCC2)=C1) `REAL300000082030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(CN2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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] 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: [11, 1, 11, 11, 53, 110, 110, 110, 110, 110, 110, 113, 113, 110, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 1, 11, 11, 11, 53, 110, 110, 110, 1, 1, 2, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 1] 402 rigid atoms, others: [1, 35, 36, 48, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 253 number of broken/clashed sets: 196 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(CN2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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] 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: [26, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 110, 110, 28, 72, 110, 110, 186, 201, 201, 201, 201, 201, 110, 27, 27, 27, 7, 1, 1, 1, 110, 110, 220, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 110] 402 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 958 number of broken/clashed sets: 196 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(CN2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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] 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: [65, 12, 65, 65, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 65, 65, 65, 135, 201, 201, 201, 12, 12, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12] 402 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48]) total number of confs: 459 number of broken/clashed sets: 196 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082030 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082030/1 /scratch/stefan/7930160/working/building/REAL300000082030 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/32 `/scratch/stefan/7930160/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C[NH+]2CCOCC2)=C1) `REAL300000082030.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C[NH+]2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 226 conformations in input total number of sets (complete confs): 226 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 35, 57, 57, 57, 57, 57, 57, 61, 61, 57, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 1, 11, 11, 11, 35, 57, 57, 57, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 1] 226 rigid atoms, others: [1, 36, 37, 49, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C[NH+]2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 226 conformations in input total number of sets (complete confs): 226 using faster count positions algorithm for large data unique positions, atoms: [19, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 57, 57, 29, 46, 57, 57, 89, 113, 113, 113, 113, 113, 113, 57, 20, 20, 20, 5, 1, 1, 1, 57, 57, 114, 89, 89, 113, 113, 113, 113, 113, 113, 113, 113, 57] 226 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 35] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 558 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082030 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C[NH+]2CCOCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 9, 6, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 226 conformations in input total number of sets (complete confs): 226 using faster count positions algorithm for large data unique positions, atoms: [46, 11, 46, 46, 93, 113, 113, 113, 113, 113, 113, 113, 113, 113, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 46, 46, 46, 93, 113, 113, 113, 11, 11, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11] 226 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49]) total number of confs: 313 number of broken/clashed sets: 118 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082030 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082030 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082030/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082030/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082030 Building REAL300000082031 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082031' /scratch/stefan/7930160/working/building/REAL300000082031 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082031 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082031/0 /scratch/stefan/7930160/working/building/REAL300000082031 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/33 `/scratch/stefan/7930160/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(CC)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000082031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082031 none CCOC1=CC=C(C(CC)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 149, 60, 60, 60, 60, 12, 12, 11, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 60, 60, 148, 160, 154, 154, 154, 154, 154, 60, 60, 20, 20, 20, 20, 20, 4, 1, 1, 1, 60, 160, 160, 160, 160, 160] 201 rigid atoms, others: [40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 504 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082031 none CCOC1=CC=C(C(CC)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 1, 1, 1, 1, 1, 1, 12, 19, 12, 12, 46, 60, 60, 60, 60, 60, 60, 73, 73, 60, 1, 1, 1, 9, 18, 20, 20, 20, 20, 20, 1, 1, 19, 19, 19, 19, 19, 46, 60, 60, 60, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 335 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082031 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082031 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082031/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082031 Building REAL300000082032 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082032' /scratch/stefan/7930160/working/building/REAL300000082032 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082032 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082032/0 /scratch/stefan/7930160/working/building/REAL300000082032 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/34 `/scratch/stefan/7930160/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1) `REAL300000082032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082032 none CC(C)CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 25, 7, 1, 7, 7, 43, 125, 125, 125, 125, 125, 125, 155, 155, 125, 1, 1, 1, 1, 1, 1, 1, 36, 36, 35, 36, 36, 36, 36, 26, 26, 25, 25, 43, 125, 125, 125, 1, 1, 1, 1] 201 rigid atoms, others: [5, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 480 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082032 none CC(C)CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 143, 116, 42, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 125, 125, 43, 53, 125, 125, 143, 143, 138, 143, 143, 143, 143, 117, 117, 116, 116, 9, 1, 1, 1, 125, 125, 125, 125] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 841 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082032 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082032 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082032/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082032 Building REAL300000082033 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082033' /scratch/stefan/7930160/working/building/REAL300000082033 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082033 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082033/0 /scratch/stefan/7930160/working/building/REAL300000082033 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/35 `/scratch/stefan/7930160/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1) `REAL300000082033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082033 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 7, 1, 7, 7, 30, 54, 54, 54, 54, 54, 54, 70, 70, 54, 1, 1, 1, 1, 1, 9, 16, 16, 9, 16, 16, 1, 1, 14, 14, 14, 14, 14, 30, 54, 54, 54, 1, 1, 16, 16, 9, 16, 16, 1, 1] 201 rigid atoms, others: [2, 37, 38, 44, 45, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 254 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: REAL300000082033 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 15, 54, 54, 15, 16, 175, 192, 192, 175, 192, 192, 54, 54, 28, 28, 28, 28, 28, 4, 1, 1, 1, 54, 54, 192, 192, 175, 192, 192, 54, 54] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 14, 36] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 479 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082033 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 57, 8, 57, 57, 153, 192, 192, 192, 192, 192, 192, 199, 199, 192, 8, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 79, 79, 79, 79, 79, 153, 192, 192, 192, 16, 16, 1, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 639 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082033 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082033 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082033/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082033 Building REAL300000082034 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082034' /scratch/stefan/7930160/working/building/REAL300000082034 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082034 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082034/0 /scratch/stefan/7930160/working/building/REAL300000082034 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/36 `/scratch/stefan/7930160/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2O)OCO3)=CC=C1F) `REAL300000082034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082034 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2O)OCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 22, 6, 1, 1, 2, 1, 1, 46, 46] 92 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 89 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: REAL300000082034 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2O)OCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'O.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 39, 39, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 9, 39, 46, 46, 92, 46, 46, 1, 1] 92 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 168 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082034 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082034 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082034/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082034 Building REAL300000082035 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082035' /scratch/stefan/7930160/working/building/REAL300000082035 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082035 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082035/0 /scratch/stefan/7930160/working/building/REAL300000082035 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/37 `/scratch/stefan/7930160/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082035 none COC1=CC(C)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 102, 102, 102, 61, 62, 62, 62, 61, 61, 61, 61, 61, 10, 1, 1, 1] 102 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 176 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: REAL300000082035 none COC1=CC(C)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 61, 61, 61, 61, 61, 61, 102, 102, 61, 4, 4, 4, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 61, 61, 61] 102 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 14, 13, 35, 36, 33, 28] set([0, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 253 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082035 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082035 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082035/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082035 Building REAL300000082036 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082036' /scratch/stefan/7930160/working/building/REAL300000082036 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082036 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082036/0 /scratch/stefan/7930160/working/building/REAL300000082036 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/38 `/scratch/stefan/7930160/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1) `REAL300000082036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082036 none CC1(C)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 114, 114, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 114, 114, 114, 114, 115, 115, 115, 115, 115, 115, 114, 114, 115, 114, 114, 51, 11, 1, 1, 1, 115, 115] 115 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) 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: REAL300000082036 none CC1(C)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 115, 115, 115, 115, 115, 115, 115, 115, 114, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 10, 49, 115, 115, 114, 1, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 41, 42, 7, 34, 35, 21, 22, 23, 24, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082036 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082036 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082036/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082036 Building REAL300000082037 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082037' /scratch/stefan/7930160/working/building/REAL300000082037 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082037 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082037/0 /scratch/stefan/7930160/working/building/REAL300000082037 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/39 `/scratch/stefan/7930160/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1)C(=O)[O-]) `REAL300000082037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082037 none CC(OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 113, 34, 34, 34, 34, 34, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 172, 201, 201, 172, 172, 172, 172, 34, 34, 34, 14, 5, 1, 1, 1, 34] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 585 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: REAL300000082037 none CC(OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 53, 53, 34, 1, 28, 38, 38, 28, 28, 28, 28, 1, 1, 1, 6, 17, 34, 34, 34, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 37, 21, 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]) total number of confs: 272 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082037 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082037 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082037/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082037 Building REAL300000082038 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082038' /scratch/stefan/7930160/working/building/REAL300000082038 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082038 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082038/0 /scratch/stefan/7930160/working/building/REAL300000082038 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/40 `/scratch/stefan/7930160/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C=C2)=CC=C1F) `REAL300000082038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082038 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 64, 87, 64, 64, 26, 5, 5, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 1, 1, 64, 64, 64, 64, 64, 26, 5, 1, 1, 22, 22, 1, 1, 64, 64] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35]) total number of confs: 272 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: REAL300000082038 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 43, 43, 64, 64, 43, 64, 160, 201, 201, 201, 201, 64, 64, 1, 1, 1, 1, 1, 9, 43, 64, 64, 201, 201, 64, 64, 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: 551 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082038 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082038 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082038/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082038 Building REAL300000082039 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082039' /scratch/stefan/7930160/working/building/REAL300000082039 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082039 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082039/0 /scratch/stefan/7930160/working/building/REAL300000082039 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/41 `/scratch/stefan/7930160/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000082039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082039 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 106, 27, 27, 27, 27, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 103, 138, 171, 171, 171, 171, 171, 27, 27, 10, 4, 1, 1, 1, 27, 138, 138, 138, 138, 138] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 741 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: REAL300000082039 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 9, 1, 1, 1, 1, 1, 1, 6, 6, 14, 27, 27, 26, 26, 27, 27, 35, 35, 27, 1, 1, 1, 9, 35, 45, 45, 45, 45, 45, 1, 1, 6, 14, 27, 27, 27, 1, 35, 35, 35, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 343 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082039 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082039 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082039/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082039 Building REAL300000082040 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082040' /scratch/stefan/7930160/working/building/REAL300000082040 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082040 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082040/0 /scratch/stefan/7930160/working/building/REAL300000082040 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/42 `/scratch/stefan/7930160/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082040 none C#CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 118, 67, 67, 77, 77, 39, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 77, 201, 201, 201, 77, 76, 38, 8, 1, 1, 1, 77, 77] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 634 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: REAL300000082040 none C#CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [13, 13, 3, 1, 1, 1, 1, 1, 1, 6, 6, 30, 76, 76, 76, 76, 76, 77, 100, 100, 76, 1, 1, 13, 13, 13, 1, 1, 6, 30, 76, 76, 76, 1, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 21, 22, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 270 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082040 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082040 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082040/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082040 Building REAL300000082041 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082041' /scratch/stefan/7930160/working/building/REAL300000082041 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082041 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082041/0 /scratch/stefan/7930160/working/building/REAL300000082041 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/43 `/scratch/stefan/7930160/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=C(C)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C) `REAL300000082041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082041 none COC(=O)COC1=C(C)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 201, 43, 43, 29, 43, 43, 43, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 201, 201, 201, 108, 108, 43, 43, 43, 43, 17, 5, 1, 1, 1, 43, 43, 43, 43] 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, 42, 43, 44]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082041 none COC(=O)COC1=C(C)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 5, 44, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 43, 43, 43, 43, 43, 43, 59, 59, 43, 1, 1, 1, 45, 45, 45, 5, 5, 2, 2, 2, 1, 6, 20, 43, 43, 43, 1, 2, 2, 2] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 41, 24, 25, 26] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082041 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082041 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082041/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082041 Building REAL300000082042 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082042' /scratch/stefan/7930160/working/building/REAL300000082042 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082042 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082042/0 /scratch/stefan/7930160/working/building/REAL300000082042 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/44 `/scratch/stefan/7930160/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082042 none COCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 126, 64, 52, 24, 24, 24, 24, 24, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 201, 201, 201, 192, 192, 126, 126, 64, 64, 24, 24, 24, 13, 5, 1, 1, 1, 24] 201 rigid atoms, others: [39, 40, 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, 38, 42]) total number of confs: 810 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082042 none COCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 55, 28, 10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 24, 24, 24, 24, 24, 31, 31, 24, 1, 87, 87, 87, 55, 55, 28, 28, 10, 10, 1, 1, 1, 6, 14, 24, 24, 24, 1] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 24, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082042 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082042 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082042/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082042 Building REAL300000082043 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082043' /scratch/stefan/7930160/working/building/REAL300000082043 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082043 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082043/0 /scratch/stefan/7930160/working/building/REAL300000082043 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/45 `/scratch/stefan/7930160/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC) `REAL300000082043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082043 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 86, 86, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 86, 86, 86, 188, 142, 142, 142, 86, 35, 9, 1, 1, 1, 86, 86, 188, 188, 188] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082043 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 86, 86, 85, 85, 86, 86, 126, 126, 86, 1, 1, 1, 1, 9, 3, 3, 3, 1, 6, 37, 86, 86, 86, 1, 1, 10, 10, 10] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 18, 19, 20, 21, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082043 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082043 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082043/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082043 Building REAL300000082044 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082044' /scratch/stefan/7930160/working/building/REAL300000082044 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082044 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082044/0 /scratch/stefan/7930160/working/building/REAL300000082044 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/46 `/scratch/stefan/7930160/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1C) `REAL300000082044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082044 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 129, 129, 129, 129, 129, 129, 201, 201, 129, 1, 1, 1, 1, 1, 4, 4, 1, 1, 1, 7, 7, 7, 33, 129, 129, 129, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 2, 2, 2] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 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, 39, 40, 41, 42, 43]) total number of confs: 528 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: REAL300000082044 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 129, 129, 129, 129, 201, 201, 129, 129, 129, 41, 41, 41, 11, 1, 1, 1, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 626 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082044 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082044 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082044/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082044 Building REAL300000082045 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082045' /scratch/stefan/7930160/working/building/REAL300000082045 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082045 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082045/0 /scratch/stefan/7930160/working/building/REAL300000082045 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/47 `/scratch/stefan/7930160/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=C1) `REAL300000082045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082045 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 45, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 11, 11, 11, 44, 85, 85, 85, 1, 4, 4, 1, 4, 4, 1] 85 rigid atoms, others: [32, 1, 38, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) 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: REAL300000082045 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [39, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 40, 40, 40, 11, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85] 85 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082045 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 13, 47, 85, 85, 85, 85, 85, 85, 85, 85, 85, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 47, 85, 85, 85, 4, 1, 1, 1, 1, 1, 4] 85 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 168 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082045 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082045 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082045/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082045 Building REAL300000082046 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082046' /scratch/stefan/7930160/working/building/REAL300000082046 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082046 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082046/0 /scratch/stefan/7930160/working/building/REAL300000082046 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/48 `/scratch/stefan/7930160/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(F)C=C2)N=C1) `REAL300000082046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082046 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 48, 135, 135, 135, 135, 135, 135, 166, 166, 135, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 1, 10, 10, 10, 48, 135, 135, 135, 2, 2, 2, 3, 3, 3, 3, 1] 166 rigid atoms, others: [1, 41, 14, 15, 16, 17, 18, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082046 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 135, 135, 135, 135, 166, 166, 166, 166, 166, 166, 135, 135, 45, 45, 45, 10, 1, 1, 1, 135, 135, 135, 166, 166, 166, 166, 135] 166 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082046 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(F)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [18, 3, 18, 18, 80, 166, 166, 166, 166, 166, 166, 166, 166, 166, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 18, 18, 80, 166, 166, 166, 3, 3, 3, 1, 1, 1, 1, 3] 166 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 323 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082046 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082046 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082046/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082046 Building REAL300000082047 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082047' /scratch/stefan/7930160/working/building/REAL300000082047 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082047 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082047/0 /scratch/stefan/7930160/working/building/REAL300000082047 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/49 `/scratch/stefan/7930160/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=CC=C23)=CC=C1F) `REAL300000082047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082047 none O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 38 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: REAL300000082047 none O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082047 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082047 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082047/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082047 Building REAL300000082048 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082048' /scratch/stefan/7930160/working/building/REAL300000082048 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082048 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082048/0 /scratch/stefan/7930160/working/building/REAL300000082048 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/50 `/scratch/stefan/7930160/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC=C23)=CC=C1F) `REAL300000082048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082048 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 38 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: REAL300000082048 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082048 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082048 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082048/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082048 Building REAL300000082049 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082049' /scratch/stefan/7930160/working/building/REAL300000082049 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082049 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082049/0 /scratch/stefan/7930160/working/building/REAL300000082049 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/51 `/scratch/stefan/7930160/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082049 none CC(C)OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 188, 201, 68, 68, 68, 68, 68, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 27, 7, 1, 1, 1, 68] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 348 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082049 none CC(C)OC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [21, 11, 21, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 68, 68, 68, 68, 68, 68, 97, 97, 68, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 32, 68, 68, 68, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 22, 38, 30, 31] set([0, 1, 2, 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: 304 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082049 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082049 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082049/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082049 Building REAL300000082050 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082050' /scratch/stefan/7930160/working/building/REAL300000082050 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082050 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082050/0 /scratch/stefan/7930160/working/building/REAL300000082050 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/52 `/scratch/stefan/7930160/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1) `REAL300000082050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082050 none CCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [37, 33, 13, 1, 13, 13, 78, 165, 165, 165, 165, 165, 165, 178, 178, 165, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 33, 33, 78, 165, 165, 165, 1, 1, 1] 201 rigid atoms, others: [19, 3, 36, 37, 16, 17, 18, 35, 20, 21, 22, 23] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 492 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082050 none CCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [67, 63, 28, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 165, 165, 67, 165, 165, 165, 165, 67, 67, 67, 67, 67, 63, 63, 7, 1, 1, 1, 165, 165, 165] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 699 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082050 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082050 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082050/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082050 Building REAL300000082051 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082051' /scratch/stefan/7930160/working/building/REAL300000082051 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082051 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082051/0 /scratch/stefan/7930160/working/building/REAL300000082051 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/53 `/scratch/stefan/7930160/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082051 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 176, 195, 163, 94, 37, 37, 37, 37, 37, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 176, 176, 163, 163, 37, 37, 37, 14, 5, 1, 1, 1, 37] 201 rigid atoms, others: [34, 35, 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, 33, 37]) total number of confs: 624 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082051 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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: [60, 38, 52, 23, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 37, 37, 37, 37, 37, 37, 50, 50, 37, 1, 38, 38, 23, 23, 1, 1, 1, 6, 19, 37, 37, 37, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 344 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082051 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082051 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082051/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082051 Building REAL300000082052 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082052' /scratch/stefan/7930160/working/building/REAL300000082052 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082052 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082052/0 /scratch/stefan/7930160/working/building/REAL300000082052 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/54 `/scratch/stefan/7930160/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=CC=C1F) `REAL300000082052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082052 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 32, 42, 32, 32, 15, 3, 3, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 13, 19, 19, 19, 1, 1, 32, 32, 32, 32, 32, 14, 3, 1, 1, 19, 13, 19, 1, 1, 32, 32] 201 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) 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: REAL300000082052 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 19, 19, 32, 32, 19, 19, 122, 201, 201, 201, 139, 201, 201, 201, 32, 32, 1, 1, 1, 1, 1, 6, 19, 32, 32, 201, 139, 201, 32, 32, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 27, 24, 25, 26, 38, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082052 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 112, 44, 44, 10, 7, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 112, 44, 20, 20, 1, 1, 1, 20, 20, 201, 201] 201 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082052 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082052 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082052/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082052 Building REAL300000082053 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082053' /scratch/stefan/7930160/working/building/REAL300000082053 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082053 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082053/0 /scratch/stefan/7930160/working/building/REAL300000082053 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/55 `/scratch/stefan/7930160/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(F)=C2)=CC=C1F) `REAL300000082053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082053 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 112, 112, 111, 111, 112, 57, 8, 1, 1, 1, 112, 112] 112 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082053 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 48, 48, 112, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 13, 48, 112, 112, 112, 1, 1] 112 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082053 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082053 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082053/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082053 Building REAL300000082054 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082054' /scratch/stefan/7930160/working/building/REAL300000082054 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082054 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082054/0 /scratch/stefan/7930160/working/building/REAL300000082054 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/56 `/scratch/stefan/7930160/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC=C23)=CC=C1F) `REAL300000082054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082054 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 54 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: REAL300000082054 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082054 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082054 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082054/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082054 Building REAL300000082055 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082055' /scratch/stefan/7930160/working/building/REAL300000082055 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082055 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082055/0 /scratch/stefan/7930160/working/building/REAL300000082055 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/57 `/scratch/stefan/7930160/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C(Cl)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082055 none COC1=C(Cl)C=C(Cl)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 51, 51, 51, 51, 36, 51, 51, 51, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 51, 51, 35, 11, 1, 1, 1] 69 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082055 none COC1=C(Cl)C=C(Cl)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 51, 51, 51, 51, 51, 51, 69, 69, 51, 3, 3, 3, 1, 1, 5, 24, 51, 51, 51] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082055 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082055 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082055/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082055 Building REAL300000082056 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082056' /scratch/stefan/7930160/working/building/REAL300000082056 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082056 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082056/0 /scratch/stefan/7930160/working/building/REAL300000082056 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/58 `/scratch/stefan/7930160/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC(F)F) `REAL300000082056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082056 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 58, 58, 58, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 58, 58, 58, 151, 189, 189, 105, 105, 105, 58, 17, 17, 17, 4, 1, 1, 1, 58, 58, 189] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 525 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082056 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 35, 58, 58, 58, 58, 58, 58, 81, 81, 58, 1, 1, 1, 1, 9, 31, 31, 3, 3, 3, 1, 11, 11, 11, 35, 58, 58, 58, 1, 1, 31] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 321 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082056 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082056 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082056/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082056 Building REAL300000082057 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082057' /scratch/stefan/7930160/working/building/REAL300000082057 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082057 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082057/0 /scratch/stefan/7930160/working/building/REAL300000082057 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/59 `/scratch/stefan/7930160/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC) `REAL300000082057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082057 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 108, 108, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 108, 108, 185, 162, 162, 162, 108, 23, 23, 23, 5, 1, 1, 1, 108, 108, 185, 185, 185] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 378 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082057 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 53, 108, 108, 108, 108, 108, 108, 152, 152, 108, 1, 1, 1, 1, 9, 3, 3, 3, 1, 13, 13, 13, 53, 108, 108, 108, 1, 1, 9, 9, 9] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 400 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082057 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082057 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082057/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082057 Building REAL300000082058 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082058' /scratch/stefan/7930160/working/building/REAL300000082058 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082058 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082058/0 /scratch/stefan/7930160/working/building/REAL300000082058 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/60 `/scratch/stefan/7930160/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000082058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082058 none CCOCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 40, 40, 40, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 28, 40, 82, 169, 169, 169, 169, 169, 120, 120, 40, 21, 5, 1, 1, 1, 40, 40, 82, 82, 82] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082058 none CCOCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 1, 1, 1, 1, 1, 7, 7, 21, 40, 40, 40, 40, 40, 40, 59, 59, 40, 1, 1, 1, 1, 3, 30, 30, 30, 29, 29, 5, 5, 1, 7, 21, 40, 40, 40, 1, 1, 3, 3, 3] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 1, 2, 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, 40, 41, 42]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082058 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082058 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082058/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082058 Building REAL300000082059 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082059' /scratch/stefan/7930160/working/building/REAL300000082059 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082059 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082059/0 /scratch/stefan/7930160/working/building/REAL300000082059 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/61 `/scratch/stefan/7930160/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1S(C)(=O)=O) `REAL300000082059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082059 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.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, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 129, 129, 129, 129, 173, 173, 173, 129, 129, 129, 129, 40, 40, 40, 9, 1, 1, 1, 129, 129, 173, 173, 173] 173 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 444 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: REAL300000082059 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.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, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 129, 129, 129, 129, 129, 129, 147, 147, 129, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 13, 13, 13, 69, 129, 129, 129, 1, 1, 5, 5, 5] 173 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 26, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 346 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082059 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082059 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082059/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082059 Building REAL300000082060 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082060' /scratch/stefan/7930160/working/building/REAL300000082060 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082060 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082060/0 /scratch/stefan/7930160/working/building/REAL300000082060 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/62 `/scratch/stefan/7930160/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOC2=O)C=C1) `REAL300000082060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082060 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 96, 96, 96, 96, 96, 96, 102, 102, 96, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 6, 6, 6, 33, 96, 96, 96, 1, 1, 7, 7, 7, 7, 1, 1] 160 rigid atoms, others: [1, 34, 33, 40, 39, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082060 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 96, 96, 45, 82, 160, 160, 160, 160, 160, 96, 96, 37, 37, 37, 10, 1, 1, 1, 96, 96, 160, 160, 160, 160, 96, 96] 160 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 442 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082060 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [25, 4, 25, 25, 82, 160, 160, 160, 160, 160, 160, 160, 160, 160, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 82, 160, 160, 160, 7, 7, 1, 1, 1, 1, 7, 7] 160 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 338 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082060 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082060 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082060/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082060 Building REAL300000082061 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082061' /scratch/stefan/7930160/working/building/REAL300000082061 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082061 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082061/0 /scratch/stefan/7930160/working/building/REAL300000082061 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/63 `/scratch/stefan/7930160/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCN(CC3=C(F)C=CC=C3Cl)CC2)=CC=C1F) `REAL300000082061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082061 none O=C([O-])C1=CC(N=NC2CCN(CC3=C(F)C=CC=C3Cl)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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: [39, 38, 39, 38, 38, 13, 13, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 7, 14, 14, 14, 1, 1, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 7, 7, 14, 9, 14, 1, 1, 1, 1, 38, 38] 188 rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 12, 40, 21, 22, 41, 39, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082061 none O=C([O-])C1=CC(N=NC2CCN(CC3=C(F)C=CC=C3Cl)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 77, 188, 188, 188, 77, 188, 188, 188, 38, 38, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 77, 77, 188, 130, 188, 38, 38, 38, 38, 1, 1] 188 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082061 none O=C([O-])C1=CC(N=NC2CCN(CC3=C(F)C=CC=C3Cl)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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, 89, 89, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 188, 188, 188, 188, 188, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 14, 14, 14, 14, 188, 188] 188 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 271 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082061 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082061 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082061/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082061 Building REAL300000082062 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082062' /scratch/stefan/7930160/working/building/REAL300000082062 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082062 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082062/0 /scratch/stefan/7930160/working/building/REAL300000082062 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/64 `/scratch/stefan/7930160/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC[NH+](C)C)C=C1) `REAL300000082062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082062 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC[NH+](C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [6, 1, 6, 6, 21, 58, 58, 58, 58, 58, 58, 77, 77, 58, 1, 1, 1, 1, 1, 5, 23, 36, 37, 37, 37, 1, 1, 6, 6, 6, 21, 58, 58, 58, 1, 1, 23, 23, 36, 36, 37, 37, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [1, 34, 35, 14, 15, 16, 17, 18, 46, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082062 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC[NH+](C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 58, 58, 26, 26, 108, 163, 201, 201, 201, 201, 58, 58, 27, 27, 27, 6, 1, 1, 1, 58, 58, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 762 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082062 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082062 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082062/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082062 Building REAL300000082063 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082063' /scratch/stefan/7930160/working/building/REAL300000082063 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082063 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082063/0 /scratch/stefan/7930160/working/building/REAL300000082063 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/65 `/scratch/stefan/7930160/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=C2C=CC(Cl)=C3Cl)=CC=C1F) `REAL300000082063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082063 none O=C([O-])C1=CC(NN=C2CCCOC3=C2C=CC(Cl)=C3Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 34, 34, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 24, 25, 26, 36]) 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: REAL300000082063 none O=C([O-])C1=CC(NN=C2CCCOC3=C2C=CC(Cl)=C3Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 34, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082063 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082063 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082063/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082063 Building REAL300000082064 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082064' /scratch/stefan/7930160/working/building/REAL300000082064 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082064 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082064/0 /scratch/stefan/7930160/working/building/REAL300000082064 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/66 `/scratch/stefan/7930160/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CCC1=CC=C(Br)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082064 none CCC(CCC1=CC=C(Br)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 57, 8, 57, 134, 162, 188, 188, 162, 174, 188, 188, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 96, 96, 96, 96, 96, 57, 146, 146, 157, 162, 188, 188, 188, 188, 1, 1, 1] 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]) total number of confs: 1144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082064 none CCC(CCC1=CC=C(Br)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 16, 72, 72, 188, 188, 188, 188, 188, 188, 201, 201, 188, 27, 27, 27, 27, 27, 16, 4, 4, 3, 3, 1, 1, 1, 1, 188, 188, 188] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082064 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082064 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082064/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082064 Building REAL300000082065 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082065' /scratch/stefan/7930160/working/building/REAL300000082065 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082065 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082065/0 /scratch/stefan/7930160/working/building/REAL300000082065 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/67 `/scratch/stefan/7930160/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C([O-])=C2)=CC=C1F) `REAL300000082065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082065 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C([O-])=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 27, 27, 28, 19, 6, 1, 1, 1, 28, 28] 28 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082065 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C([O-])=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 7, 22, 28, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082065 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082065 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082065/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082065 Building REAL300000082066 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082066' /scratch/stefan/7930160/working/building/REAL300000082066 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082066 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082066/0 /scratch/stefan/7930160/working/building/REAL300000082066 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/68 `/scratch/stefan/7930160/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCC2=CC=CC=N2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082066 none COC1=CC=C(OCC2=CC=CC=N2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [108, 91, 91, 91, 91, 38, 9, 1, 1, 1, 1, 1, 1, 1, 91, 91, 126, 126, 166, 198, 198, 198, 198, 198, 198, 201, 201, 198, 91, 108, 108, 108, 91, 91, 9, 9, 1, 1, 1, 1, 126, 166, 198, 198, 198, 91] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082066 none COC1=CC=C(OCC2=CC=CC=N2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 8, 35, 91, 91, 91, 91, 91, 1, 1, 4, 4, 15, 28, 28, 28, 28, 28, 28, 34, 34, 28, 1, 3, 3, 3, 1, 1, 35, 35, 91, 91, 91, 91, 4, 15, 28, 28, 28, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 45, 14, 15, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082066 none COC1=CC=C(OCC2=CC=CC=N2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [31, 28, 28, 28, 28, 28, 28, 64, 142, 198, 198, 198, 198, 198, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 31, 31, 31, 28, 28, 142, 142, 198, 198, 198, 198, 18, 7, 1, 1, 1, 28] 201 rigid atoms, others: [42, 43, 44, 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, 45]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082066 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082066 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082066/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082066 Building REAL300000082067 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082067' /scratch/stefan/7930160/working/building/REAL300000082067 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082067 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082067/0 /scratch/stefan/7930160/working/building/REAL300000082067 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/69 `/scratch/stefan/7930160/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082067 none CSC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 134, 134, 134, 57, 57, 57, 57, 57, 57, 57, 57, 57, 11, 1, 1, 1] 134 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 204 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: REAL300000082067 none CSC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 57, 57, 57, 57, 57, 57, 94, 94, 57, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 57, 57, 57] 134 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 241 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082067 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082067 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082067/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082067 Building REAL300000082068 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082068' /scratch/stefan/7930160/working/building/REAL300000082068 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082068 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082068/0 /scratch/stefan/7930160/working/building/REAL300000082068 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/70 `/scratch/stefan/7930160/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000082068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082068 none C=C(C)COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 179, 191, 87, 28, 28, 28, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 28, 28, 53, 191, 191, 191, 191, 191, 179, 179, 28, 15, 5, 1, 1, 1, 28, 28, 53, 53, 53] 201 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082068 none C=C(C)COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 51, 89, 9, 1, 1, 1, 1, 1, 6, 6, 16, 28, 28, 27, 27, 28, 28, 36, 36, 28, 1, 1, 1, 1, 3, 89, 89, 90, 90, 90, 51, 51, 1, 6, 16, 28, 28, 28, 1, 1, 3, 3, 3] 201 rigid atoms, others: [33, 4, 5, 6, 7, 8, 39, 40, 21, 22, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082068 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082068 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082068/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082068 Building REAL300000082069 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082069' /scratch/stefan/7930160/working/building/REAL300000082069 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082069 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082069/0 /scratch/stefan/7930160/working/building/REAL300000082069 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/71 `/scratch/stefan/7930160/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)COC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082069 none CCOC(=O)COC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 201, 81, 35, 35, 35, 35, 35, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 201, 201, 201, 201, 201, 93, 93, 35, 35, 35, 16, 16, 16, 5, 1, 1, 1, 35] 201 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 495 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082069 none CCOC(=O)COC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 11, 46, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 35, 35, 35, 35, 35, 35, 39, 39, 35, 1, 67, 67, 67, 67, 67, 11, 11, 1, 1, 1, 7, 7, 7, 20, 35, 35, 35, 1] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 44, 26] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 334 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082069 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082069 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082069/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082069 Building REAL300000082070 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082070' /scratch/stefan/7930160/working/building/REAL300000082070 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082070 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082070/0 /scratch/stefan/7930160/working/building/REAL300000082070 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/72 `/scratch/stefan/7930160/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082070 none CCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 196, 192, 177, 104, 82, 30, 30, 30, 30, 30, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 201, 201, 201, 201, 201, 200, 200, 192, 192, 177, 177, 104, 104, 30, 30, 30, 13, 5, 1, 1, 1, 30] 201 rigid atoms, others: [46, 44, 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, 40, 41, 42, 43, 47]) total number of confs: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082070 none CCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 38, 29, 10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 30, 30, 30, 30, 30, 30, 40, 40, 30, 1, 50, 50, 50, 49, 49, 46, 46, 38, 38, 29, 29, 10, 10, 1, 1, 1, 6, 18, 30, 30, 30, 1] 201 rigid atoms, others: [11, 6, 39, 8, 9, 10, 7, 12, 47, 40, 41, 25] set([0, 1, 2, 3, 4, 5, 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, 42, 43, 44, 45, 46]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082070 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082070 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082070/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082070 Building REAL300000082071 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082071' /scratch/stefan/7930160/working/building/REAL300000082071 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082071 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082071/0 /scratch/stefan/7930160/working/building/REAL300000082071 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/73 `/scratch/stefan/7930160/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(OC)=C1O) `REAL300000082071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082071 none C=CCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [157, 97, 56, 56, 56, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 98, 56, 56, 157, 157, 157, 97, 97, 56, 23, 7, 1, 1, 1, 56, 98, 98, 98, 112] 402 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 723 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082071 none C=CCC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 6, 6, 26, 56, 56, 55, 55, 56, 56, 88, 88, 56, 1, 1, 1, 3, 1, 1, 14, 14, 14, 5, 5, 1, 6, 26, 56, 56, 56, 1, 3, 3, 3, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 23, 24, 36, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 284 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082071 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082071 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082071/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082071 Building REAL300000082072 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082072' /scratch/stefan/7930160/working/building/REAL300000082072 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082072 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082072/0 /scratch/stefan/7930160/working/building/REAL300000082072 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/74 `/scratch/stefan/7930160/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C12) `REAL300000082072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082072 none CC1=NN(C)C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 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, 129, 129, 129, 57, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 129, 129, 129, 129, 129, 129, 129, 129, 129, 57, 13, 1, 1, 1, 129] 129 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082072 none CC1=NN(C)C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 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, 1, 1, 1, 10, 10, 57, 129, 129, 128, 128, 129, 129, 129, 129, 129, 1, 1, 2, 2, 2, 2, 2, 2, 1, 10, 57, 129, 129, 129, 1] 129 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 36, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082072 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082072 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082072/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082072 Building REAL300000082073 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082073' /scratch/stefan/7930160/working/building/REAL300000082073 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082073 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082073/0 /scratch/stefan/7930160/working/building/REAL300000082073 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/75 `/scratch/stefan/7930160/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=NN1C1=CC=CC=C1) `REAL300000082073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082073 none CC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 138, 54, 8, 54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 138, 138, 138, 138, 201, 201, 138, 201, 201, 138, 138, 138, 54, 54, 54, 54, 1, 1, 1, 201, 201, 138, 201, 201] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 604 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082073 none CC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 49, 49, 138, 138, 138, 138, 138, 138, 200, 200, 138, 1, 1, 1, 1, 5, 5, 1, 5, 5, 2, 2, 2, 8, 8, 8, 8, 138, 138, 138, 5, 5, 1, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 462 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082073 none CC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 20, 20, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 201, 201, 201, 1, 1, 1, 1, 1] 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]) total number of confs: 325 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082073 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082073 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082073/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082073 Building REAL300000082074 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082074' /scratch/stefan/7930160/working/building/REAL300000082074 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082074 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082074/0 /scratch/stefan/7930160/working/building/REAL300000082074 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/76 `/scratch/stefan/7930160/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CN=C2)S1) `REAL300000082074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082074 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 1, 10, 10, 58, 135, 135, 135, 135, 135, 135, 155, 155, 135, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 1, 10, 10, 10, 58, 135, 135, 135, 2, 2, 2, 5, 5, 4, 5] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 346 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082074 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 135, 41, 41, 41, 8, 1, 1, 1, 135, 135, 135, 201, 201, 201, 201] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 321 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082074 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 5, 35, 35, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 35, 35, 35, 124, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [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, 35]) total number of confs: 430 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082074 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082074 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082074/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082074 Building REAL300000082075 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082075' /scratch/stefan/7930160/working/building/REAL300000082075 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082075 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082075/0 /scratch/stefan/7930160/working/building/REAL300000082075 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/77 `/scratch/stefan/7930160/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082075 none CN1CCCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 118, 118, 119, 119, 119, 118, 118, 118, 118, 118, 118, 118, 52, 11, 1, 1, 1, 118, 118] 119 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 188 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082075 none CN1CCCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 118, 118, 118, 118, 118, 118, 119, 119, 118, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 10, 54, 118, 118, 118, 1, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 40, 21, 22, 23, 39, 33, 27, 28, 29, 30, 31] set([34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 225 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082075 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082075 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082075/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082075 Building REAL300000082076 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082076' /scratch/stefan/7930160/working/building/REAL300000082076 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082076 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082076/0 /scratch/stefan/7930160/working/building/REAL300000082076 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/78 `/scratch/stefan/7930160/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)F)=C2)=CC=C1F) `REAL300000082076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082076 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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: [61, 46, 61, 46, 46, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 12, 47, 47, 1, 46, 46, 45, 45, 46, 24, 6, 1, 1, 1, 47, 1, 46, 46] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 26, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 31]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082076 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 5, 20, 20, 46, 46, 46, 46, 46, 163, 201, 201, 46, 1, 1, 1, 1, 1, 5, 20, 46, 46, 46, 201, 46, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082076 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082076 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082076/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082076 Building REAL300000082077 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082077' /scratch/stefan/7930160/working/building/REAL300000082077 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082077 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082077/0 /scratch/stefan/7930160/working/building/REAL300000082077 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/79 `/scratch/stefan/7930160/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000082077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082077 none CCCCCOC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 193, 187, 129, 68, 19, 19, 19, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 19, 19, 19, 36, 193, 193, 193, 193, 193, 193, 193, 193, 193, 129, 129, 19, 7, 5, 1, 1, 1, 19, 19, 36, 36, 36] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082077 none CCCCCOC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 78, 69, 37, 10, 1, 1, 1, 1, 1, 7, 7, 14, 19, 19, 19, 19, 19, 19, 22, 22, 19, 1, 1, 1, 1, 3, 78, 78, 78, 78, 78, 78, 78, 78, 78, 37, 37, 1, 7, 14, 19, 19, 19, 1, 1, 3, 3, 3] 201 rigid atoms, others: [5, 38, 7, 8, 9, 44, 45, 22, 23, 24, 25, 6] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082077 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082077 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082077/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082077 Building REAL300000082078 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082078' /scratch/stefan/7930160/working/building/REAL300000082078 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082078 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082078/0 /scratch/stefan/7930160/working/building/REAL300000082078 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/80 `/scratch/stefan/7930160/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(Br)C=C1O) `REAL300000082078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082078 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [167, 143, 143, 143, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 143, 143, 143, 143, 143, 167, 167, 167, 143, 57, 11, 1, 1, 1, 143, 286] 334 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082078 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 54, 143, 143, 143, 143, 143, 143, 167, 167, 143, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 54, 143, 143, 143, 1, 2] 334 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 33]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082078 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082078 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082078/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082078 Building REAL300000082079 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082079' /scratch/stefan/7930160/working/building/REAL300000082079 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082079 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082079/0 /scratch/stefan/7930160/working/building/REAL300000082079 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/81 `/scratch/stefan/7930160/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(O)C(Cl)=C2)=CC=C1F) `REAL300000082079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082079 none O=C([O-])C1=CC(NN=CC2=CC=C(O)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 55, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 110, 110, 111, 55, 9, 1, 1, 2, 1, 111, 111] 222 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 26, 28, 29]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082079 none O=C([O-])C1=CC(NN=CC2=CC=C(O)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 52, 52, 111, 111, 92, 111, 111, 111, 111, 1, 1, 1, 1, 1, 12, 52, 111, 111, 222, 111, 1, 1] 222 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082079 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082079/1 /scratch/stefan/7930160/working/building/REAL300000082079 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/82 `/scratch/stefan/7930160/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([O-])C(Cl)=C2)=CC=C1F) `REAL300000082079.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082079 none O=C([O-])C1=CC(NN=CC2=CC=C([O-])C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 49, 49, 50, 42, 10, 1, 1, 1, 50, 50] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082079 none O=C([O-])C1=CC(NN=CC2=CC=C([O-])C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 4, 22, 22, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 22, 50, 50, 50, 1, 1] 50 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082079 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082079 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082079/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082079/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082079 Building REAL300000082080 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082080' /scratch/stefan/7930160/working/building/REAL300000082080 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082080 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082080/0 /scratch/stefan/7930160/working/building/REAL300000082080 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/83 `/scratch/stefan/7930160/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCCC#N) `REAL300000082080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082080 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCCC#N 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 18, 18, 18, 18, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 18, 18, 18, 78, 112, 157, 189, 189, 38, 38, 38, 18, 18, 9, 5, 1, 1, 1, 18, 112, 112, 165, 165, 183, 183] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 731 number of broken/clashed sets: 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: REAL300000082080 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCCC#N 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 18, 18, 17, 17, 18, 18, 21, 21, 18, 1, 1, 1, 9, 31, 51, 85, 84, 4, 4, 4, 1, 1, 6, 12, 18, 18, 18, 1, 31, 31, 63, 63, 77, 77] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 37, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 458 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082080 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082080 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082080/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082080 Building REAL300000082081 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082081' /scratch/stefan/7930160/working/building/REAL300000082081 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082081 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082081/0 /scratch/stefan/7930160/working/building/REAL300000082081 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/84 `/scratch/stefan/7930160/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082081 none CCOC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 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.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 192, 129, 129, 129, 129, 129, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 129, 201, 201, 201, 201, 201, 129, 129, 129, 26, 26, 26, 7, 1, 1, 1, 129] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 339 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082081 none CCOC1=CC=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 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.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [12, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 55, 129, 129, 129, 129, 129, 129, 175, 175, 129, 1, 12, 12, 12, 12, 12, 1, 1, 1, 13, 13, 13, 55, 129, 129, 129, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 38, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 462 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082081 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082081 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082081/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082081 Building REAL300000082082 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082082' /scratch/stefan/7930160/working/building/REAL300000082082 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082082 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082082/0 /scratch/stefan/7930160/working/building/REAL300000082082 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/85 `/scratch/stefan/7930160/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC=C(F)C=C23)=CC=C1F) `REAL300000082082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082082 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 119, 119, 120, 57, 10, 1, 1, 1, 1, 1, 120, 120] 120 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082082 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 52, 52, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 13, 52, 120, 120, 120, 120, 120, 1, 1] 120 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082082 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082082 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082082/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082082 Building REAL300000082083 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082083' /scratch/stefan/7930160/working/building/REAL300000082083 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082083 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082083/0 /scratch/stefan/7930160/working/building/REAL300000082083 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/86 `/scratch/stefan/7930160/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(NS(C)(=O)=O)C=C1) `REAL300000082083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082083 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(NS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 84, 84, 84, 84, 84, 84, 119, 119, 84, 1, 1, 1, 1, 1, 11, 27, 27, 27, 1, 1, 6, 6, 6, 33, 84, 84, 84, 1, 1, 11, 27, 27, 27, 1, 1] 201 rigid atoms, others: [32, 1, 38, 33, 39, 14, 15, 16, 17, 18, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 382 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082083 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(NS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 84, 84, 56, 84, 176, 201, 201, 201, 84, 84, 33, 33, 33, 6, 1, 1, 1, 84, 84, 176, 201, 201, 201, 84, 84] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 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: 700 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082083 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082083 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082083/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082083 Building REAL300000082084 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082084' /scratch/stefan/7930160/working/building/REAL300000082084 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082084 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082084/0 /scratch/stefan/7930160/working/building/REAL300000082084 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/87 `/scratch/stefan/7930160/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCOC2=O)=C1) `REAL300000082084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082084 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCOC2=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 105, 105, 105, 105, 105, 105, 118, 118, 105, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 11, 11, 11, 51, 105, 105, 105, 1, 1, 1, 7, 7, 7, 7, 1] 201 rigid atoms, others: [1, 34, 35, 33, 40, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 269 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082084 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCOC2=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 105, 105, 105, 105, 105, 201, 201, 201, 201, 201, 105, 25, 25, 25, 7, 1, 1, 1, 105, 105, 105, 201, 201, 201, 201, 105] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 308 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082084 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCOC2=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 45, 45, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 132, 201, 201, 201, 6, 7, 7, 1, 1, 1, 1, 7] 201 rigid atoms, others: [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, 35, 40]) total number of confs: 442 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082084 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082084 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082084/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082084 Building REAL300000082085 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082085' /scratch/stefan/7930160/working/building/REAL300000082085 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082085 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082085/0 /scratch/stefan/7930160/working/building/REAL300000082085 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/88 `/scratch/stefan/7930160/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082085 none CC1=CC=C(Cl)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 29, 29, 28, 12, 1, 1, 1] 29 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082085 none CC1=CC=C(Cl)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28, 29, 29, 28, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/7930160/working/building/REAL300000082085 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082085 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082085/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082085 Building REAL300000082086 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082086' /scratch/stefan/7930160/working/building/REAL300000082086 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082086 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082086/0 /scratch/stefan/7930160/working/building/REAL300000082086 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/89 `/scratch/stefan/7930160/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F) `REAL300000082086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 36, 36, 36, 36, 36, 7, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 36, 36] 47 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 47, 47, 46, 47, 47, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 47, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 18, 4, 4, 3, 3, 3, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 47, 47, 47, 47, 47, 18, 3, 3, 4, 4, 4, 4, 1, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082086 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082086/1 /scratch/stefan/7930160/working/building/REAL300000082086 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/90 `/scratch/stefan/7930160/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F) `REAL300000082086.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 35, 48, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 35, 35] 48 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 48, 48, 35, 48, 48, 35, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 48, 48, 35, 48, 48, 1, 1] 48 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082086 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 48, 48] 48 rigid atoms, others: [35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082086 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082086 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082086/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082086/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082086 Building REAL300000082087 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082087' /scratch/stefan/7930160/working/building/REAL300000082087 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082087 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082087/0 /scratch/stefan/7930160/working/building/REAL300000082087 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/91 `/scratch/stefan/7930160/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082087 none CCCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 183, 177, 167, 112, 84, 28, 28, 28, 28, 28, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 201, 201, 201, 201, 201, 201, 201, 189, 189, 177, 177, 167, 167, 112, 112, 28, 28, 28, 11, 5, 1, 1, 1, 28] 201 rigid atoms, others: [48, 49, 47, 16, 17, 18, 19, 20, 21, 22, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50]) total number of confs: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082087 none CCCCCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 37, 27, 10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 28, 28, 28, 28, 28, 28, 37, 37, 28, 1, 64, 64, 64, 63, 63, 63, 63, 49, 49, 37, 37, 27, 27, 10, 10, 1, 1, 1, 6, 16, 28, 28, 28, 1] 201 rigid atoms, others: [43, 7, 8, 9, 42, 11, 12, 13, 44, 50, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082087 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082087 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082087/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082087 Building REAL300000082088 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082088' /scratch/stefan/7930160/working/building/REAL300000082088 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082088 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082088/0 /scratch/stefan/7930160/working/building/REAL300000082088 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/92 `/scratch/stefan/7930160/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCC(C)C) `REAL300000082088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082088 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCC(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 22, 22, 84, 143, 187, 187, 187, 42, 42, 42, 22, 22, 9, 5, 1, 1, 1, 22, 143, 143, 187, 187, 187, 187, 187, 187, 187, 187, 187] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082088 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OCCC(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 22, 22, 21, 21, 22, 22, 29, 29, 22, 1, 1, 1, 9, 38, 60, 61, 61, 3, 3, 3, 1, 1, 6, 14, 22, 22, 22, 1, 38, 38, 60, 60, 61, 61, 61, 61, 61, 61, 61] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 37, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082088 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082088 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082088/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082088 Building REAL300000082089 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082089' /scratch/stefan/7930160/working/building/REAL300000082089 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082089 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082089/0 /scratch/stefan/7930160/working/building/REAL300000082089 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/93 `/scratch/stefan/7930160/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082089 none CC1=CC=C(F)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [29, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 29, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 30, 29, 12, 1, 1, 1] 30 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082089 none CC1=CC=C(F)C2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 29, 29, 30, 30, 30, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082089 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082089 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082089/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082089 Building REAL300000082090 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082090' /scratch/stefan/7930160/working/building/REAL300000082090 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082090 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082090/0 /scratch/stefan/7930160/working/building/REAL300000082090 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/94 `/scratch/stefan/7930160/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCC(F)(F)F) `REAL300000082090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082090 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 32, 32, 32, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 32, 32, 113, 197, 197, 197, 197, 77, 77, 77, 32, 13, 5, 1, 1, 1, 32, 32, 197, 197] 201 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082090 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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 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, 18, 32, 32, 32, 32, 32, 32, 47, 47, 32, 1, 1, 1, 1, 9, 35, 35, 35, 35, 3, 3, 3, 1, 7, 18, 32, 32, 32, 1, 1, 35, 35] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 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, 38, 39]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082090 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082090 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082090/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082090 Building REAL300000082091 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082091' /scratch/stefan/7930160/working/building/REAL300000082091 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082091 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082091/0 /scratch/stefan/7930160/working/building/REAL300000082091 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/95 `/scratch/stefan/7930160/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3)S2)=CC=C1F) `REAL300000082091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082091 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 98, 70, 70, 32, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 70, 70, 70, 70, 70, 32, 7, 1, 1, 12, 12, 12, 12, 70, 70] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082091 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 38, 38, 70, 70, 70, 70, 201, 201, 201, 201, 201, 201, 70, 1, 1, 1, 1, 1, 8, 38, 70, 70, 201, 201, 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: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082091 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 135, 47, 47, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 135, 47, 12, 12, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082091 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082091 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082091/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082091 Building REAL300000082092 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082092' /scratch/stefan/7930160/working/building/REAL300000082092 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082092 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082092/0 /scratch/stefan/7930160/working/building/REAL300000082092 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/96 `/scratch/stefan/7930160/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=CC=C2O)=CC=C1F) `REAL300000082092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082092 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=CC=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [107, 80, 107, 80, 80, 38, 11, 11, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 1, 80, 80, 80, 80, 80, 38, 11, 1, 3, 3, 2, 3, 3, 1, 1, 2, 80, 80] 214 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082092 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=CC=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 47, 47, 80, 80, 80, 107, 107, 80, 107, 107, 80, 80, 80, 80, 1, 1, 1, 1, 1, 10, 47, 80, 107, 107, 80, 107, 107, 80, 80, 160, 1, 1] 214 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 422 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082092 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=CC=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 58, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 107, 107, 107, 107, 107, 58, 15, 3, 1, 1, 1, 1, 1, 3, 3, 6, 107, 107] 214 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082092 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082092 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082092/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082092 Building REAL300000082093 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082093' /scratch/stefan/7930160/working/building/REAL300000082093 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082093 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082093/0 /scratch/stefan/7930160/working/building/REAL300000082093 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/97 `/scratch/stefan/7930160/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082093 none CCOC1=C(OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 103, 52, 48, 82, 82, 116, 82, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 116, 165, 165, 165, 165, 165, 116, 116, 116, 82, 27, 9, 1, 1, 1, 82, 116, 116, 116] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 756 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082093 none CCOC1=C(OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 2, 1, 1, 1, 1, 3, 1, 1, 1, 9, 9, 37, 82, 82, 81, 81, 82, 82, 129, 129, 82, 1, 1, 1, 3, 14, 14, 14, 13, 13, 4, 4, 4, 1, 9, 37, 82, 82, 82, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 7, 8, 9, 34, 40, 22, 23, 24] set([0, 1, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 405 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082093 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082093 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082093/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082093 Building REAL300000082094 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082094' /scratch/stefan/7930160/working/building/REAL300000082094 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082094 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082094/0 /scratch/stefan/7930160/working/building/REAL300000082094 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/98 `/scratch/stefan/7930160/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C)S1) `REAL300000082094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082094 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 59, 121, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 59, 121, 121, 120, 2, 2, 2, 2, 2, 2] 121 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20] set([0, 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]) 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: REAL300000082094 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', '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, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 120, 120, 120, 120, 120, 120, 57, 57, 57, 10, 1, 1, 1, 121, 121, 121, 121, 121, 121] 121 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082094 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082094 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082094/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082094 Building REAL300000082095 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082095' /scratch/stefan/7930160/working/building/REAL300000082095 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082095 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082095/0 /scratch/stefan/7930160/working/building/REAL300000082095 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/99 `/scratch/stefan/7930160/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082095 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 165, 49, 165, 49, 49, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 49, 201, 201, 201, 201, 201, 49, 49, 49, 49, 49, 49, 1, 1, 1, 49, 49, 49, 49] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082095 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 34, 12, 1, 12, 1, 1, 1, 1, 1, 13, 13, 49, 49, 49, 49, 49, 49, 67, 67, 49, 1, 1, 57, 57, 57, 56, 56, 1, 1, 1, 1, 1, 1, 49, 49, 49, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 40, 37, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 34, 35, 36]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082095 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082095 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082095/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082095 Building REAL300000082096 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082096' /scratch/stefan/7930160/working/building/REAL300000082096 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082096 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082096/0 /scratch/stefan/7930160/working/building/REAL300000082096 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/100 `/scratch/stefan/7930160/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC(SC(F)F)=CC=C32)=CC=C1F) `REAL300000082096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082096 none O=C([O-])C1=CC(NN=C2CCCC3=CC(SC(F)F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 51, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 48, 48, 1, 1, 1, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 48, 1, 1, 29, 29] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 36, 37] set([0, 1, 2, 3, 4, 5, 38, 39, 16, 17, 18, 35, 22, 23, 24, 25, 26, 27]) total number of confs: 282 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: REAL300000082096 none O=C([O-])C1=CC(NN=C2CCCC3=CC(SC(F)F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 29, 29, 29, 29, 29, 29, 29, 152, 201, 201, 29, 29, 29, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 201, 29, 29, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 489 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082096 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082096 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082096/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082096 Building REAL300000082097 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082097' /scratch/stefan/7930160/working/building/REAL300000082097 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082097 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082097/0 /scratch/stefan/7930160/working/building/REAL300000082097 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/101 `/scratch/stefan/7930160/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000082097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082097 none CCC(C)OC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 172, 132, 172, 41, 41, 41, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 41, 41, 81, 190, 190, 190, 190, 190, 172, 172, 172, 172, 41, 13, 5, 1, 1, 1, 41, 41, 81, 81, 81] 201 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 586 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: REAL300000082097 none CCC(C)OC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 21, 9, 21, 1, 1, 1, 1, 1, 6, 6, 14, 41, 41, 40, 40, 41, 41, 62, 62, 41, 1, 1, 1, 1, 3, 40, 40, 40, 40, 40, 21, 21, 21, 21, 1, 6, 14, 41, 41, 41, 1, 1, 4, 4, 4] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 357 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082097 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082097 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082097/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082097 Building REAL300000082098 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082098' /scratch/stefan/7930160/working/building/REAL300000082098 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082098 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082098/0 /scratch/stefan/7930160/working/building/REAL300000082098 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/102 `/scratch/stefan/7930160/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082098 none CC1=CC(Cl)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 1, 1, 1] 44 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 70 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: REAL300000082098 none CC1=CC(Cl)=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 68 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082098 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082098 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082098/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082098 Building REAL300000082099 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082099' /scratch/stefan/7930160/working/building/REAL300000082099 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082099 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082099/0 /scratch/stefan/7930160/working/building/REAL300000082099 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/103 `/scratch/stefan/7930160/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082099 none COC(=O)C1=CC=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 61, 114, 61, 61, 61, 61, 61, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 114, 114, 114, 61, 61, 122, 31, 8, 1, 1, 1, 61] 228 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 389 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082099 none COC(=O)C1=CC=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 61, 61, 61, 61, 61, 61, 87, 87, 61, 1, 13, 13, 13, 1, 1, 2, 8, 28, 61, 61, 61, 1] 228 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082099 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082099/1 /scratch/stefan/7930160/working/building/REAL300000082099 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/104 `/scratch/stefan/7930160/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C([O-])C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082099.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082099 none COC(=O)C1=CC=C([O-])C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 26, 49, 26, 26, 26, 26, 26, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 49, 49, 49, 26, 26, 16, 8, 1, 1, 1, 26] 49 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082099 none COC(=O)C1=CC=C([O-])C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 26, 26, 26, 26, 26, 26, 32, 32, 26, 1, 13, 13, 13, 1, 1, 4, 10, 26, 26, 26, 1] 49 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082099 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082099 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082099/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082099/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082099 Building REAL300000082100 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082100' /scratch/stefan/7930160/working/building/REAL300000082100 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082100 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082100/0 /scratch/stefan/7930160/working/building/REAL300000082100 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/105 `/scratch/stefan/7930160/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082100 none N#CCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 163, 106, 79, 34, 34, 34, 34, 34, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 201, 201, 163, 163, 106, 106, 34, 34, 34, 19, 7, 1, 1, 1, 34] 201 rigid atoms, others: [36, 37, 38, 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, 39]) total number of confs: 770 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: REAL300000082100 none N#CCCCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 32, 14, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 46, 46, 34, 1, 56, 56, 32, 32, 14, 14, 1, 1, 1, 6, 17, 34, 34, 34, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 24, 39, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 372 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082100 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082100 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082100/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082100 Building REAL300000082101 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082101' /scratch/stefan/7930160/working/building/REAL300000082101 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082101 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082101/0 /scratch/stefan/7930160/working/building/REAL300000082101 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/106 `/scratch/stefan/7930160/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082101 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 97, 49, 97, 49, 49, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 49, 49, 1, 1, 1, 49, 49, 49, 49] 201 rigid atoms, others: [39, 40, 41, 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, 35, 36, 37, 38, 42, 43, 44, 45]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082101 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 25, 24, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 49, 49, 49, 49, 49, 49, 74, 74, 49, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 49, 49, 49, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 44, 45, 43, 23, 24, 42, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082101 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082101 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082101/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082101 Building REAL300000082102 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082102' /scratch/stefan/7930160/working/building/REAL300000082102 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082102 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082102/0 /scratch/stefan/7930160/working/building/REAL300000082102 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/107 `/scratch/stefan/7930160/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC(O)=CC=C32)=CC=C1F) `REAL300000082102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082102 none O=C([O-])C1=CC(NN=C2CCCC3=CC(O)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 35, 35] 70 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 32, 19, 20, 21, 22, 23, 24, 36]) total number of confs: 55 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: REAL300000082102 none O=C([O-])C1=CC(NN=C2CCCC3=CC(O)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 70, 35, 35, 1, 1] 70 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082102 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082102 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082102/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082102 Building REAL300000082103 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082103' /scratch/stefan/7930160/working/building/REAL300000082103 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082103 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082103/0 /scratch/stefan/7930160/working/building/REAL300000082103 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/108 `/scratch/stefan/7930160/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(Cl)C=CC(Cl)=C23)=CC=C1F) `REAL300000082103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082103 none O=C([O-])C1=CC(NN=C2CCOC3=C(Cl)C=CC(Cl)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 12, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 40, 40] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 57 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: REAL300000082103 none O=C([O-])C1=CC(NN=C2CCOC3=C(Cl)C=CC(Cl)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 12, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 1, 1] 40 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082103 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082103 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082103/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082103 Building REAL300000082104 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082104' /scratch/stefan/7930160/working/building/REAL300000082104 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082104 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082104/0 /scratch/stefan/7930160/working/building/REAL300000082104 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/109 `/scratch/stefan/7930160/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000082104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082104 none CSCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 14, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 1, 6, 6, 40, 110, 110, 110, 110, 110, 110, 145, 145, 110, 1, 1, 1, 1, 1, 1, 76, 76, 76, 26, 26, 40, 110, 110, 110, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 35, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 484 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082104 none CSCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 14, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 110, 110, 32, 110, 110, 162, 162, 162, 98, 98, 8, 1, 1, 1, 110, 110, 32, 110, 110] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 671 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082104 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082104 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082104/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082104 Building REAL300000082105 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082105' /scratch/stefan/7930160/working/building/REAL300000082105 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082105 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082105/0 /scratch/stefan/7930160/working/building/REAL300000082105 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/110 `/scratch/stefan/7930160/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082105 none CCOC1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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, 142, 79, 79, 79, 43, 79, 79, 79, 79, 79, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 168, 168, 168, 168, 168, 79, 79, 79, 40, 8, 1, 1, 1] 168 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082105 none CCOC1=CC=C([N+](=O)[O-])C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 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: [27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 79, 79, 79, 79, 79, 79, 111, 111, 79, 28, 28, 28, 27, 27, 1, 1, 1, 12, 35, 79, 79, 79] 168 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082105 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082105 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082105/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082105 Building REAL300000082106 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082106' /scratch/stefan/7930160/working/building/REAL300000082106 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082106 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082106/0 /scratch/stefan/7930160/working/building/REAL300000082106 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/111 `/scratch/stefan/7930160/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(Cl)=C32)=CC=C1F) `REAL300000082106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082106 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 7, 1, 1, 1, 1, 28, 28] 29 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082106 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 28, 1, 1, 1, 1, 1, 12, 28, 28, 29, 29, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082106 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082106 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082106/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082106 Building REAL300000082107 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082107' /scratch/stefan/7930160/working/building/REAL300000082107 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082107 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082107/0 /scratch/stefan/7930160/working/building/REAL300000082107 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/112 `/scratch/stefan/7930160/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(C)=C1Cl)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2) `REAL300000082107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082107 none CC1=CC2=C(C(C)=C1Cl)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 1, 1, 1, 44, 44, 44, 44] 44 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 71 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: REAL300000082107 none CC1=CC2=C(C(C)=C1Cl)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 44, 44, 44, 1, 1, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 36, 38, 28, 39, 37] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082107 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082107 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082107/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082107 Building REAL300000082108 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082108' /scratch/stefan/7930160/working/building/REAL300000082108 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082108 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082108/0 /scratch/stefan/7930160/working/building/REAL300000082108 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/113 `/scratch/stefan/7930160/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=C2)=CC=C1F) `REAL300000082108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082108 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 53, 22, 6, 1, 2, 2, 2, 2, 1, 53, 53] 53 rigid atoms, others: [33, 8, 9, 10, 11, 12, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 34, 35]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082108 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 31, 31, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 11, 31, 53, 53, 53, 53, 53, 53, 1, 1] 53 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082108 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 53, 53, 53, 53, 53, 23, 7, 2, 1, 1, 1, 1, 2, 53, 53] 53 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082108 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082108 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082108/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082108 Building REAL300000082109 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082109' /scratch/stefan/7930160/working/building/REAL300000082109 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082109 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082109/0 /scratch/stefan/7930160/working/building/REAL300000082109 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/114 `/scratch/stefan/7930160/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1[O-]) `REAL300000082109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082109 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 41, 41, 41, 1, 1] 41 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 71 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082109 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 41, 41, 41, 41, 41, 41, 41, 41, 35, 35, 35, 8, 1, 1, 1, 41, 41] 41 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082109 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082109 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082109/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082109 Building REAL300000082110 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082110' /scratch/stefan/7930160/working/building/REAL300000082110 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082110 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082110/0 /scratch/stefan/7930160/working/building/REAL300000082110 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/115 `/scratch/stefan/7930160/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2C)C=C1) `REAL300000082110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082110 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 28, 66, 66, 66, 66, 66, 66, 82, 82, 66, 1, 1, 1, 1, 1, 2, 2, 14, 14, 2, 14, 14, 14, 1, 1, 5, 5, 5, 28, 66, 66, 66, 1, 1, 2, 2, 14, 14, 2, 14, 15, 15, 15, 1, 1] 201 rigid atoms, others: [1, 36, 37, 48, 47, 14, 15, 16, 17, 18, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 222 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082110 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 66, 66, 27, 27, 94, 94, 201, 201, 166, 201, 201, 201, 66, 66, 28, 28, 28, 6, 1, 1, 1, 66, 66, 94, 94, 201, 201, 167, 201, 201, 201, 201, 66, 66] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 35] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 504 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082110 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 7, 44, 44, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 44, 44, 44, 129, 201, 201, 201, 14, 14, 7, 7, 1, 1, 1, 1, 2, 2, 2, 14, 14] 201 rigid atoms, others: [40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082110 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082110 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082110/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082110 Building REAL300000082111 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082111' /scratch/stefan/7930160/working/building/REAL300000082111 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082111 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082111/0 /scratch/stefan/7930160/working/building/REAL300000082111 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/116 `/scratch/stefan/7930160/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCC[NH+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082111 none COC(=O)CCC[NH+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 1, 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, 201, 109, 201, 57, 49, 29, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 201, 201, 201, 109, 109, 57, 57, 49, 49, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [40, 41, 42, 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, 38, 39, 43, 44, 45, 46]) total number of confs: 840 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: REAL300000082111 none COC(=O)CCC[NH+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 1, 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: [35, 35, 9, 35, 5, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 29, 29, 29, 29, 29, 29, 40, 40, 29, 1, 1, 35, 35, 35, 9, 9, 5, 5, 3, 3, 1, 1, 1, 1, 1, 29, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 46, 44, 43, 24, 25, 38, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082111 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082111 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082111/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082111 Building REAL300000082112 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082112' /scratch/stefan/7930160/working/building/REAL300000082112 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082112 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082112/0 /scratch/stefan/7930160/working/building/REAL300000082112 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/117 `/scratch/stefan/7930160/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C(F)=C2)=CC=C1F) `REAL300000082112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082112 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 38, 8, 1, 1, 62, 62] 62 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082112 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 45, 45, 62, 62, 62, 46, 62, 62, 62, 62, 1, 1, 1, 1, 1, 13, 45, 62, 62, 1, 1] 62 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082112 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082112 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082112/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082112 Building REAL300000082113 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082113' /scratch/stefan/7930160/working/building/REAL300000082113 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082113 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082113/0 /scratch/stefan/7930160/working/building/REAL300000082113 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/118 `/scratch/stefan/7930160/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F) `REAL300000082113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082113 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 49, 37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 37, 37, 37, 37, 37, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 37, 37] 49 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41]) 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: REAL300000082113 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 49, 49, 37, 49, 49, 49, 37, 1, 1, 1, 1, 1, 11, 37, 37, 37, 37, 37, 37, 49, 49, 49, 49, 1, 1] 49 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082113 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 49, 49, 49, 49, 49, 18, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 49, 49] 49 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082113 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082113/1 /scratch/stefan/7930160/working/building/REAL300000082113 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/119 `/scratch/stefan/7930160/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F) `REAL300000082113.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082113 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 45, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 34, 34] 45 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082113 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 45, 45, 34, 45, 45, 45, 34, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082113 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=C(F)C=C2)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082113 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082113 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082113/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082113/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082113 Building REAL300000082114 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082114' /scratch/stefan/7930160/working/building/REAL300000082114 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082114 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082114/0 /scratch/stefan/7930160/working/building/REAL300000082114 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/120 `/scratch/stefan/7930160/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1) `REAL300000082114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082114 none CCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 21, 9, 1, 9, 49, 49, 146, 146, 146, 146, 146, 146, 180, 180, 146, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 21, 21, 9, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [19, 33, 34, 3, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 471 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: REAL300000082114 none CCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 123, 57, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 138, 146, 146, 146, 137, 157, 157, 157, 152, 157, 133, 133, 57, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1036 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082114 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082114 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082114/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082114 Building REAL300000082115 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082115' /scratch/stefan/7930160/working/building/REAL300000082115 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082115 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082115/0 /scratch/stefan/7930160/working/building/REAL300000082115 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/121 `/scratch/stefan/7930160/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1O) `REAL300000082115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082115 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 53, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 97, 97, 97, 1, 1, 1, 2] 194 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 197 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: REAL300000082115 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 97, 97, 83, 97, 97, 97, 97, 45, 45, 45, 11, 1, 1, 1, 97, 97, 97, 194] 194 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 418 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082115 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082115/1 /scratch/stefan/7930160/working/building/REAL300000082115 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/122 `/scratch/stefan/7930160/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1[O-]) `REAL300000082115.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082115 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 14, 38, 38, 38, 1, 1, 1] 38 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082115 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 9, 1, 1, 1, 38, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082115 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082115 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082115/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082115/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082115 Building REAL300000082116 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082116' /scratch/stefan/7930160/working/building/REAL300000082116 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082116 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082116/0 /scratch/stefan/7930160/working/building/REAL300000082116 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/123 `/scratch/stefan/7930160/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1I) `REAL300000082116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082116 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1I NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 38, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 82, 82, 82, 1, 1, 1, 1] 82 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000082116 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1I NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 82, 82, 75, 82, 82, 82, 48, 48, 48, 12, 1, 1, 1, 82, 82, 77, 82] 82 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082116 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082116 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082116/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082116 Building REAL300000082117 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082117' /scratch/stefan/7930160/working/building/REAL300000082117 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082117 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082117/0 /scratch/stefan/7930160/working/building/REAL300000082117 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/124 `/scratch/stefan/7930160/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C) `REAL300000082117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082117 none COC(=O)CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 201, 91, 38, 38, 38, 38, 38, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 201, 201, 201, 130, 130, 91, 91, 38, 38, 38, 9, 5, 1, 1, 1, 38, 38, 38] 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, 42, 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: REAL300000082117 none COC(=O)CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 12, 63, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 38, 38, 38, 38, 38, 38, 47, 47, 38, 1, 1, 64, 64, 64, 12, 12, 5, 5, 2, 2, 2, 9, 21, 38, 38, 38, 2, 2, 2] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 24, 25] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082117 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082117 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082117/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082117 Building REAL300000082118 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082118' /scratch/stefan/7930160/working/building/REAL300000082118 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082118 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082118/0 /scratch/stefan/7930160/working/building/REAL300000082118 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/125 `/scratch/stefan/7930160/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CCCCC2)=CC=C1F) `REAL300000082118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082118 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [138, 113, 138, 113, 113, 36, 36, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 23, 24, 24, 113, 113, 113, 113, 113, 9, 3, 3, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 23, 24, 24, 24, 24, 113, 113] 165 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 319 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082118 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 49, 99, 113, 113, 105, 113, 113, 49, 115, 122, 122, 122, 119, 1, 1, 1, 1, 1, 49, 99, 99, 113, 113, 113, 113, 113, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1] 165 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 728 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082118 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [143, 122, 143, 122, 122, 39, 39, 8, 1, 8, 19, 24, 24, 21, 24, 24, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 8, 19, 19, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 122] 165 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47]) total number of confs: 340 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082118 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082118 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082118/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082118 Building REAL300000082119 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082119' /scratch/stefan/7930160/working/building/REAL300000082119 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082119 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082119/0 /scratch/stefan/7930160/working/building/REAL300000082119 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/126 `/scratch/stefan/7930160/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=CC=C1F) `REAL300000082119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082119 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 131, 131, 130, 130, 131, 58, 10, 1, 1, 1, 131, 131] 131 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000082119 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 56, 56, 131, 131, 94, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 13, 56, 131, 131, 131, 1, 1] 131 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: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082119 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082119 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082119/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082119 Building REAL300000082120 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082120' /scratch/stefan/7930160/working/building/REAL300000082120 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082120 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082120/0 /scratch/stefan/7930160/working/building/REAL300000082120 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/127 `/scratch/stefan/7930160/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F) `REAL300000082120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082120 none CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 59, 64, 59, 59, 59, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 59, 59, 64, 64, 64, 64, 64, 64, 59, 59, 25, 7, 1, 1, 1, 59] 64 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) 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: REAL300000082120 none CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 40, 59, 59, 59, 59, 59, 59, 64, 64, 59, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 10, 39, 59, 59, 59, 1] 64 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 36, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082120 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082120 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082120/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082120 Building REAL300000082121 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082121' /scratch/stefan/7930160/working/building/REAL300000082121 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082121 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082121/0 /scratch/stefan/7930160/working/building/REAL300000082121 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/128 `/scratch/stefan/7930160/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(Br)C=C23)=CC=C1F) `REAL300000082121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082121 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 30, 30] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 42 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: REAL300000082121 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 1, 1] 30 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 53 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082121 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082121 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082121/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082121 Building REAL300000082122 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082122' /scratch/stefan/7930160/working/building/REAL300000082122 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082122 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082122/0 /scratch/stefan/7930160/working/building/REAL300000082122 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/129 `/scratch/stefan/7930160/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)C(F)=C2)=CC=C1F) `REAL300000082122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082122 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [95, 71, 95, 71, 71, 37, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 71, 71, 71, 71, 71, 37, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 71, 71] 105 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 242 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: REAL300000082122 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 27, 27, 71, 71, 71, 71, 105, 105, 105, 105, 105, 71, 71, 71, 1, 1, 1, 1, 1, 7, 27, 71, 71, 105, 105, 105, 105, 105, 105, 105, 105, 71, 1, 1] 105 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082122 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 68, 20, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 105, 105, 105, 105, 105, 68, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 105, 105] 105 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082122 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082122 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082122/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082122 Building REAL300000082123 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082123' /scratch/stefan/7930160/working/building/REAL300000082123 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082123 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082123/0 /scratch/stefan/7930160/working/building/REAL300000082123 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/130 `/scratch/stefan/7930160/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl) `REAL300000082123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082123 none C=CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 188, 116, 43, 36, 43, 43, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 201, 201, 201, 188, 188, 43, 43, 18, 5, 1, 1, 1, 43] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082123 none C=CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [50, 25, 7, 1, 1, 1, 1, 1, 1, 6, 6, 21, 43, 43, 42, 42, 43, 43, 67, 67, 43, 1, 1, 1, 50, 50, 50, 25, 25, 1, 1, 6, 21, 43, 43, 43, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 23, 36, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082123 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082123 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082123/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082123 Building REAL300000082124 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082124' /scratch/stefan/7930160/working/building/REAL300000082124 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082124 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082124/0 /scratch/stefan/7930160/working/building/REAL300000082124 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/131 `/scratch/stefan/7930160/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)(F)F)=C2)=CC=C1F) `REAL300000082124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082124 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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: [85, 56, 85, 56, 56, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 12, 25, 24, 25, 1, 56, 56, 55, 55, 56, 29, 6, 1, 1, 1, 1, 56, 56] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000082124 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 5, 21, 21, 56, 56, 56, 56, 56, 201, 201, 201, 201, 56, 1, 1, 1, 1, 1, 5, 21, 56, 56, 56, 56, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082124 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082124 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082124/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082124 Building REAL300000082125 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082125' /scratch/stefan/7930160/working/building/REAL300000082125 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082125 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082125/0 /scratch/stefan/7930160/working/building/REAL300000082125 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/132 `/scratch/stefan/7930160/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=C(F)C=C2)C=C1) `REAL300000082125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082125 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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: [6, 1, 6, 6, 34, 107, 107, 107, 107, 107, 107, 141, 141, 107, 1, 1, 1, 1, 1, 2, 6, 16, 16, 6, 16, 16, 16, 1, 1, 7, 7, 7, 33, 107, 107, 107, 1, 1, 6, 6, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [1, 36, 37, 44, 45, 14, 15, 16, 17, 18, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 394 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: REAL300000082125 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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: [37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 107, 107, 64, 107, 158, 169, 201, 201, 169, 201, 201, 201, 107, 107, 38, 38, 38, 8, 1, 1, 1, 107, 107, 169, 169, 201, 201, 201, 201, 107, 107] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 35] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 729 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082125 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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: [47, 16, 47, 47, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 47, 47, 47, 135, 201, 201, 201, 16, 16, 3, 3, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 457 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082125 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082125 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082125/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082125 Building REAL300000082126 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082126' /scratch/stefan/7930160/working/building/REAL300000082126 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082126 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082126/0 /scratch/stefan/7930160/working/building/REAL300000082126 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/133 `/scratch/stefan/7930160/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(C)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C) `REAL300000082126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082126 none CCN1C(C)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 37, 37, 37, 37, 37, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 66, 66, 66, 66, 66, 37, 37, 37, 37, 23, 8, 1, 1, 1, 37, 37, 37] 66 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082126 none CCN1C(C)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 6, 22, 37, 37, 37, 2, 2, 2] 66 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082126 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082126 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082126/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082126 Building REAL300000082127 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082127' /scratch/stefan/7930160/working/building/REAL300000082127 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082127 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082127/0 /scratch/stefan/7930160/working/building/REAL300000082127 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/134 `/scratch/stefan/7930160/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C)=C1) `REAL300000082127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082127 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 156, 156, 156, 156, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 156, 156, 156, 1, 1, 2, 2, 2, 2, 1] 312 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 286 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: REAL300000082127 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 156, 156, 96, 130, 156, 156, 156, 51, 51, 51, 11, 1, 1, 1, 156, 156, 312, 156, 156, 156, 156] 312 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 757 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082127 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082127 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082127/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082127 Building REAL300000082128 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082128' /scratch/stefan/7930160/working/building/REAL300000082128 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082128 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082128/0 /scratch/stefan/7930160/working/building/REAL300000082128 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/135 `/scratch/stefan/7930160/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082128 none CCCC(CC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 97, 46, 8, 46, 117, 120, 120, 120, 120, 120, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 123, 123, 123, 123, 117, 109, 109, 46, 117, 117, 120, 120, 120, 120, 120, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37]) total number of confs: 882 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082128 none CCCC(CC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 1, 1, 1, 1, 1, 1, 8, 39, 39, 120, 120, 120, 120, 120, 120, 164, 164, 120, 29, 29, 29, 29, 29, 23, 23, 8, 3, 3, 1, 1, 1, 1, 1, 120, 120, 120] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 454 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082128 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082128 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082128/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082128 Building REAL300000082129 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082129' /scratch/stefan/7930160/working/building/REAL300000082129 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082129 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082129/0 /scratch/stefan/7930160/working/building/REAL300000082129 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/136 `/scratch/stefan/7930160/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CC=C3)S2)=CC=C1F) `REAL300000082129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082129 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 117, 121, 117, 117, 48, 10, 10, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 117, 117, 117, 117, 117, 47, 10, 1, 4, 4, 1, 4, 4, 117, 117] 121 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082129 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 56, 56, 117, 117, 117, 117, 121, 121, 117, 121, 121, 117, 1, 1, 1, 1, 1, 13, 56, 117, 121, 121, 117, 121, 121, 1, 1] 121 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082129 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 77, 19, 19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 121, 121, 121, 121, 121, 77, 19, 4, 1, 1, 1, 1, 1, 121, 121] 121 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 256 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082129 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082129 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082129/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082129 Building REAL300000082130 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082130' /scratch/stefan/7930160/working/building/REAL300000082130 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082130 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082130/0 /scratch/stefan/7930160/working/building/REAL300000082130 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/137 `/scratch/stefan/7930160/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=C(C)C([N+](=O)[O-])=C1C) `REAL300000082130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082130 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 48, 154, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 48, 154, 154, 154, 1, 2, 2, 2, 2, 2, 2] 154 rigid atoms, others: [1, 35, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 277 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: REAL300000082130 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 154, 154, 154, 154, 154, 72, 108, 154, 154, 154, 154, 154, 154, 53, 53, 53, 11, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154] 154 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 705 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082130 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082130 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082130/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082130 Building REAL300000082131 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082131' /scratch/stefan/7930160/working/building/REAL300000082131 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082131 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082131/0 /scratch/stefan/7930160/working/building/REAL300000082131 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/138 `/scratch/stefan/7930160/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082131 none CC(C)CCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [92, 78, 92, 57, 38, 38, 38, 38, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 92, 92, 92, 92, 78, 78, 57, 57, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1] 92 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082131 none CC(C)CCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 38, 38, 40, 40, 38, 8, 8, 8, 8, 8, 8, 8, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38] 92 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082131 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082131 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082131/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082131 Building REAL300000082132 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082132' /scratch/stefan/7930160/working/building/REAL300000082132 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082132 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082132/0 /scratch/stefan/7930160/working/building/REAL300000082132 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/139 `/scratch/stefan/7930160/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(F)=C1) `REAL300000082132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082132 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 66, 156, 156, 156, 156, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 156, 156, 156, 1, 1, 2, 1] 312 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 291 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: REAL300000082132 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 156, 156, 156, 156, 156, 156, 156, 55, 55, 55, 11, 1, 1, 1, 156, 156, 312, 156] 312 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 547 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082132 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082132 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082132/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082132 Building REAL300000082133 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082133' /scratch/stefan/7930160/working/building/REAL300000082133 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082133 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082133/0 /scratch/stefan/7930160/working/building/REAL300000082133 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/140 `/scratch/stefan/7930160/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=CC=CC=C32)=CC=C1F) `REAL300000082133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082133 none O=C([O-])C1=CC(NN=C2CCCOC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 31, 32, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 23, 24, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082133 none O=C([O-])C1=CC(NN=C2CCCOC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082133 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082133 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082133/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082133 Building REAL300000082134 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082134' /scratch/stefan/7930160/working/building/REAL300000082134 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082134 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082134/0 /scratch/stefan/7930160/working/building/REAL300000082134 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/141 `/scratch/stefan/7930160/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC(C)=C2)C=C1) `REAL300000082134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082134 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC(C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 48, 48, 48, 48, 48, 48, 68, 68, 48, 1, 1, 1, 1, 1, 2, 2, 15, 15, 3, 15, 15, 15, 1, 1, 6, 6, 6, 24, 48, 48, 48, 1, 1, 2, 2, 15, 15, 2, 16, 16, 16, 15, 1, 1] 201 rigid atoms, others: [1, 36, 37, 48, 47, 14, 15, 16, 17, 18, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300000082134 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC(C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 48, 48, 32, 48, 73, 73, 201, 201, 141, 201, 201, 201, 48, 48, 22, 22, 22, 4, 1, 1, 1, 48, 48, 73, 73, 201, 201, 143, 201, 201, 201, 201, 48, 48] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13, 35] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 509 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082134 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC(C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 15, 58, 58, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 58, 58, 58, 128, 201, 201, 201, 15, 15, 8, 8, 1, 1, 1, 2, 2, 2, 1, 15, 15] 201 rigid atoms, others: [40, 41, 42, 46, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 47, 48]) total number of confs: 492 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082134 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082134 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082134/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082134 Building REAL300000082135 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082135' /scratch/stefan/7930160/working/building/REAL300000082135 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082135 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082135/0 /scratch/stefan/7930160/working/building/REAL300000082135 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/142 `/scratch/stefan/7930160/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(C)C=C2)S1) `REAL300000082135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082135 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 57, 160, 160, 160, 160, 160, 160, 169, 169, 159, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 10, 10, 10, 57, 160, 160, 159, 2, 2, 2, 3, 3, 4, 4, 4, 3, 3] 169 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082135 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 159, 160, 159, 159, 159, 168, 169, 168, 168, 168, 168, 159, 56, 56, 56, 10, 1, 1, 1, 160, 160, 160, 169, 169, 169, 169, 169, 168, 168] 169 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082135 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [26, 3, 26, 26, 98, 169, 169, 169, 169, 169, 169, 169, 169, 168, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 27, 27, 27, 98, 169, 169, 168, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 169 rigid atoms, others: [37, 38, 42, 43, 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, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 378 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082135 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082135 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082135/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082135 Building REAL300000082136 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082136' /scratch/stefan/7930160/working/building/REAL300000082136 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082136 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082136/0 /scratch/stefan/7930160/working/building/REAL300000082136 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/143 `/scratch/stefan/7930160/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC3=C(S2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1) `REAL300000082136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 38, 38, 38, 38, 47, 47, 38, 1, 1, 1, 3, 3, 4, 4, 4, 3, 3, 7, 38, 38, 38, 1, 1, 1, 1, 1, 1, 3, 3] 47 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 41, 23, 24, 25, 38, 42, 39, 37] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44]) 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: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 21, 47, 47, 47, 4, 4, 4, 4, 5, 5, 1, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 44, 26, 27, 31] set([6, 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, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 47, 47, 38, 38, 38, 38, 38, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 38, 47, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 38, 38, 38, 38, 38, 38, 47, 47] 47 rigid atoms, others: [34, 35, 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, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082136 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082136/1 /scratch/stefan/7930160/working/building/REAL300000082136 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/144 `/scratch/stefan/7930160/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC3=C(S2)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1) `REAL300000082136.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 45, 45, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 34, 34, 34, 1, 1, 1, 1, 1, 1, 4, 4] 45 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 10, 11, 40, 41, 23, 24, 25, 38, 42, 39, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 43, 44]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 4, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 45, 45, 45, 4, 4, 4, 4, 4, 4, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 44, 26, 27, 31] set([6, 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, 42]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082136 none CC1=CC=C(C2=NC3=C(S2)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CCC3)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 34, 45, 45, 34, 34, 34, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 45, 45, 45, 45, 45, 45, 45, 34, 1, 1, 1, 34, 34, 34, 34, 34, 34, 45, 45] 45 rigid atoms, others: [34, 35, 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, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 160 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082136 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082136 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082136/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082136/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082136 Building REAL300000082137 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082137' /scratch/stefan/7930160/working/building/REAL300000082137 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082137 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082137/0 /scratch/stefan/7930160/working/building/REAL300000082137 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/145 `/scratch/stefan/7930160/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1CCCCC1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082137 none CC(CCC1CCCCC1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 56, 119, 129, 200, 201, 201, 200, 200, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 56, 126, 126, 129, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 813 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082137 none CC(CCC1CCCCC1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 25, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 24, 25, 25, 25, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 36, 38, 37, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082137 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082137 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082137/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082137 Building REAL300000082138 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082138' /scratch/stefan/7930160/working/building/REAL300000082138 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082138 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082138/0 /scratch/stefan/7930160/working/building/REAL300000082138 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/146 `/scratch/stefan/7930160/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=CC=C(F)C=C32)=CC=C1F) `REAL300000082138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082138 none O=C([O-])C1=CC(NN=C2CCOC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 55 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: REAL300000082138 none O=C([O-])C1=CC(NN=C2CCOC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082138 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082138 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082138/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082138 Building REAL300000082139 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082139' /scratch/stefan/7930160/working/building/REAL300000082139 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082139 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082139/0 /scratch/stefan/7930160/working/building/REAL300000082139 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/147 `/scratch/stefan/7930160/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1F) `REAL300000082139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082139 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 54, 111, 111, 111, 1, 1, 2, 1] 222 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 219 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: REAL300000082139 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 111, 111, 45, 111, 111, 111, 111, 45, 45, 45, 11, 1, 1, 1, 111, 111, 222, 111] 222 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 639 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082139 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082139 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082139/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082139 Building REAL300000082140 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082140' /scratch/stefan/7930160/working/building/REAL300000082140 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082140 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082140/0 /scratch/stefan/7930160/working/building/REAL300000082140 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/148 `/scratch/stefan/7930160/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F) `REAL300000082140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 71, 102, 71, 71, 20, 4, 4, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 71, 71, 71, 71, 71, 20, 4, 7, 7, 1, 7, 7, 1, 1, 71, 71] 105 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 54, 54, 71, 71, 71, 105, 105, 71, 105, 105, 71, 71, 1, 1, 1, 1, 1, 11, 54, 105, 105, 71, 105, 105, 71, 71, 1, 1] 105 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 105, 105, 63, 15, 15, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 105, 105, 105, 105, 105, 63, 15, 1, 1, 1, 1, 1, 7, 7, 105, 105] 105 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082140 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082140/1 /scratch/stefan/7930160/working/building/REAL300000082140 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/149 `/scratch/stefan/7930160/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F) `REAL300000082140.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 125, 169, 125, 125, 44, 44, 6, 1, 1, 1, 1, 1, 7, 7, 3, 7, 7, 1, 1, 125, 125, 125, 125, 125, 6, 6, 7, 7, 4, 7, 7, 1, 1, 125, 125] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 54, 125, 125, 122, 201, 201, 190, 201, 201, 125, 125, 1, 1, 1, 1, 1, 53, 54, 201, 201, 197, 201, 201, 125, 125, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082140 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 149, 149, 26, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 26, 26, 1, 1, 1, 1, 1, 7, 7, 201, 201] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 326 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082140 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082140 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082140/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082140/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082140 Building REAL300000082141 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082141' /scratch/stefan/7930160/working/building/REAL300000082141 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082141 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082141/0 /scratch/stefan/7930160/working/building/REAL300000082141 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/150 `/scratch/stefan/7930160/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1) `REAL300000082141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082141 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 45, 77, 77, 77, 77, 77, 77, 84, 84, 76, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 1, 1, 10, 10, 10, 45, 77, 77, 76, 2, 2, 2, 5, 5, 5, 5, 1] 201 rigid atoms, others: [1, 41, 14, 15, 16, 17, 18, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000082141 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 76, 77, 76, 76, 201, 201, 191, 201, 201, 201, 76, 76, 28, 28, 28, 5, 1, 1, 1, 77, 77, 77, 201, 201, 201, 201, 77] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 346 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082141 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC(Cl)=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 37, 37, 141, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 141, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 5] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 447 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082141 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082141 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082141/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082141 Building REAL300000082142 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082142' /scratch/stefan/7930160/working/building/REAL300000082142 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082142 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082142/0 /scratch/stefan/7930160/working/building/REAL300000082142 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/151 `/scratch/stefan/7930160/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082142 none CC(C#N)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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, 139, 201, 201, 65, 62, 81, 81, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 81, 81, 201, 201, 201, 201, 81, 81, 36, 9, 1, 1, 1, 81, 81] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) 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: REAL300000082142 none CC(C#N)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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: [15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 8, 8, 34, 81, 81, 81, 81, 81, 81, 116, 116, 81, 1, 1, 15, 15, 15, 15, 1, 1, 8, 34, 81, 81, 81, 1, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 22, 23, 36, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082142 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082142 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082142/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082142 Building REAL300000082143 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082143' /scratch/stefan/7930160/working/building/REAL300000082143 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082143 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082143/0 /scratch/stefan/7930160/working/building/REAL300000082143 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/152 `/scratch/stefan/7930160/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=CN2CC(F)(F)F)=CC=C1F) `REAL300000082143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082143 none O=C([O-])C1=CC(NN=CC2=NC=CN2CC(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [122, 102, 122, 102, 102, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 102, 102, 102, 102, 102, 29, 7, 1, 1, 6, 6, 102, 102] 159 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082143 none O=C([O-])C1=CC(NN=CC2=NC=CN2CC(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 61, 61, 102, 102, 102, 102, 102, 159, 159, 159, 159, 1, 1, 1, 1, 1, 13, 61, 102, 102, 159, 159, 1, 1] 159 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082143 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082143/1 /scratch/stefan/7930160/working/building/REAL300000082143 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/153 `/scratch/stefan/7930160/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC=CN2CC(F)(F)F)=CC=C1F) `REAL300000082143.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082143 none O=C([O-])C1=CC(N=NCC2=NC=CN2CC(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 115, 154, 115, 115, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 115, 115, 115, 115, 115, 9, 9, 1, 1, 6, 6, 115, 115] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082143 none O=C([O-])C1=CC(N=NCC2=NC=CN2CC(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 45, 115, 115, 115, 115, 115, 201, 201, 201, 201, 1, 1, 1, 1, 1, 45, 45, 115, 115, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082143 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082143 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082143/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082143/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082143 Building REAL300000082144 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082144' /scratch/stefan/7930160/working/building/REAL300000082144 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082144 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082144/0 /scratch/stefan/7930160/working/building/REAL300000082144 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/154 `/scratch/stefan/7930160/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000082144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082144 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 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, 27, 12, 12, 27, 27, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 34, 34, 27, 27, 12, 4, 1, 1, 1, 27] 34 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) 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: REAL300000082144 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] 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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 27, 27, 26, 26, 27, 27, 31, 31, 27, 1, 1, 1, 2, 2, 5, 5, 1, 1, 6, 14, 27, 27, 27, 1] 34 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 36, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082144 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082144 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082144/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082144 Building REAL300000082145 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082145' /scratch/stefan/7930160/working/building/REAL300000082145 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082145 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082145/0 /scratch/stefan/7930160/working/building/REAL300000082145 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/155 `/scratch/stefan/7930160/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=CC=C1F) `REAL300000082145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082145 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [134, 102, 134, 102, 102, 43, 11, 11, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 102, 102, 102, 102, 102, 43, 11, 1, 4, 4, 4, 4, 4, 102, 102] 178 rigid atoms, others: [8, 9, 10, 11, 12, 13, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082145 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 11, 62, 62, 102, 102, 102, 102, 178, 178, 178, 178, 178, 178, 178, 178, 102, 1, 1, 1, 1, 1, 11, 62, 102, 178, 178, 178, 178, 178, 1, 1] 178 rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 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, 35]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082145 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 95, 28, 28, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 178, 178, 178, 178, 178, 95, 28, 4, 1, 1, 1, 1, 1, 178, 178] 178 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082145 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082145 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082145/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082145 Building REAL300000082146 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082146' /scratch/stefan/7930160/working/building/REAL300000082146 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082146 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082146/0 /scratch/stefan/7930160/working/building/REAL300000082146 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/156 `/scratch/stefan/7930160/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CS3)=N2)=CC=C1F) `REAL300000082146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082146 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CS3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [124, 98, 124, 98, 98, 40, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 98, 98, 98, 98, 98, 39, 6, 1, 12, 12, 12, 98, 98] 191 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) 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: REAL300000082146 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CS3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 59, 59, 98, 98, 98, 98, 191, 191, 191, 191, 98, 1, 1, 1, 1, 1, 11, 59, 98, 191, 191, 191, 1, 1] 191 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082146 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CS3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 191, 191, 132, 35, 35, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 191, 191, 191, 191, 191, 131, 35, 12, 1, 1, 1, 191, 191] 191 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082146 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082146 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082146/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082146 Building REAL300000082147 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082147' /scratch/stefan/7930160/working/building/REAL300000082147 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082147 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082147/0 /scratch/stefan/7930160/working/building/REAL300000082147 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/157 `/scratch/stefan/7930160/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2)=CC=C1F) `REAL300000082147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082147 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 23, 23] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 32 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: REAL300000082147 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082147 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 8, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 33 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082147 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082147 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082147/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082147 Building REAL300000082148 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082148' /scratch/stefan/7930160/working/building/REAL300000082148 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082148 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082148/0 /scratch/stefan/7930160/working/building/REAL300000082148 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/158 `/scratch/stefan/7930160/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082148 none CCCCCCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 158, 112, 74, 62, 41, 41, 41, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 195, 201, 201, 201, 201, 161, 161, 112, 112, 74, 74, 62, 62, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1] 201 rigid atoms, others: [45, 12, 44, 13, 14, 15, 16, 17, 18, 19, 46, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 990 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082148 none CCCCCCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 5, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 41, 41, 41, 41, 41, 41, 56, 56, 41, 29, 32, 32, 32, 32, 20, 20, 11, 11, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41] 201 rigid atoms, others: [11, 36, 5, 6, 7, 8, 9, 10, 39, 40, 43, 41, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082148 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082148 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082148/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082148 Building REAL300000082149 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082149' /scratch/stefan/7930160/working/building/REAL300000082149 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082149 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082149/0 /scratch/stefan/7930160/working/building/REAL300000082149 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/159 `/scratch/stefan/7930160/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC1=CC=CC(Cl)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082149 none CC(C)CC(CC1=CC=CC(Cl)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 74, 75, 47, 8, 47, 92, 170, 170, 170, 170, 170, 170, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 75, 75, 75, 75, 74, 74, 47, 92, 92, 170, 170, 170, 170, 1, 1, 1] 201 rigid atoms, others: [41, 42, 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, 40]) total number of confs: 672 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: REAL300000082149 none CC(C)CC(CC1=CC=CC(Cl)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 23, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 57, 57, 170, 170, 170, 170, 170, 170, 181, 181, 170, 23, 23, 23, 23, 23, 23, 23, 22, 22, 13, 5, 5, 1, 1, 1, 1, 170, 170, 170] 201 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 12, 40, 38, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082149 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082149 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082149/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082149 Building REAL300000082150 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082150' /scratch/stefan/7930160/working/building/REAL300000082150 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082150 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082150/0 /scratch/stefan/7930160/working/building/REAL300000082150 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/160 `/scratch/stefan/7930160/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1O) `REAL300000082150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082150 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 95, 95, 95, 1, 1, 2, 2, 2, 2, 2, 2, 2] 190 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082150 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 95, 95, 83, 95, 95, 95, 95, 95, 39, 39, 39, 10, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 190] 190 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 396 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082150 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082150 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082150/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082150 Building REAL300000082151 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082151' /scratch/stefan/7930160/working/building/REAL300000082151 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082151 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082151/0 /scratch/stefan/7930160/working/building/REAL300000082151 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/161 `/scratch/stefan/7930160/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(C)C)C=C1) `REAL300000082151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082151 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 85, 85, 85, 85, 85, 85, 123, 123, 85, 1, 1, 1, 1, 1, 9, 22, 22, 1, 1, 5, 5, 5, 29, 85, 85, 85, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [32, 1, 40, 41, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 370 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: REAL300000082151 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 85, 85, 28, 53, 188, 201, 201, 85, 85, 29, 29, 29, 6, 1, 1, 1, 85, 85, 201, 201, 201, 201, 201, 201, 201, 85, 85] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 541 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082151 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082151 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082151/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082151 Building REAL300000082152 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082152' /scratch/stefan/7930160/working/building/REAL300000082152 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082152 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082152/0 /scratch/stefan/7930160/working/building/REAL300000082152 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/162 `/scratch/stefan/7930160/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082152 none CCC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 39, 39, 39, 39, 39, 39, 39, 39, 38, 39, 39, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 78, 78, 78, 78, 39, 39, 39, 39, 13, 1, 1, 1] 78 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082152 none CCC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 39, 39, 38, 38, 39, 39, 42, 42, 39, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 39, 39, 39] 78 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082152 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082152 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082152/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082152 Building REAL300000082153 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082153' /scratch/stefan/7930160/working/building/REAL300000082153 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082153 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082153/0 /scratch/stefan/7930160/working/building/REAL300000082153 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/163 `/scratch/stefan/7930160/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082153 none CCS(=O)(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 155, 192, 192, 101, 53, 101, 101, 29, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 101, 201, 201, 201, 201, 201, 155, 101, 101, 29, 29, 29, 7, 1, 1, 1, 101, 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, 42]) total number of confs: 769 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082153 none CCS(=O)(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 12, 12, 12, 49, 101, 101, 101, 101, 101, 101, 132, 132, 101, 1, 1, 22, 22, 22, 22, 22, 6, 1, 1, 12, 12, 12, 49, 101, 101, 101, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 41, 24, 25, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 421 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082153 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082153 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082153/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082153 Building REAL300000082154 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082154' /scratch/stefan/7930160/working/building/REAL300000082154 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082154 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082154/0 /scratch/stefan/7930160/working/building/REAL300000082154 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/164 `/scratch/stefan/7930160/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=CC=C2)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082154 none CC1(C2=CC=CC=C2)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 38, 38, 72, 72, 72, 72, 72, 72, 72, 72, 72, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 72, 72, 72, 5, 5] 72 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30] set([0, 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, 38]) total number of confs: 108 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082154 none CC1(C2=CC=CC=C2)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 12, 12, 45, 45, 45, 45, 45, 45, 57, 57, 45, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 1, 1, 45, 45, 45, 1, 1] 72 rigid atoms, others: [0, 1, 2, 33, 38, 32, 8, 9, 10, 22, 37, 31] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082154 none CC1(C2=CC=CC=C2)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 72, 72, 72, 72, 72, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 45, 45, 45, 72, 72, 72, 72, 72, 45, 45, 45, 1, 1, 1, 45, 45] 72 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 149 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082154 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082154 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082154/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082154 Building REAL300000082155 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082155' /scratch/stefan/7930160/working/building/REAL300000082155 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082155 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082155/0 /scratch/stefan/7930160/working/building/REAL300000082155 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/165 `/scratch/stefan/7930160/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082155 none CC(C)(C)OC(=O)N1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 175, 198, 198, 90, 53, 90, 53, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 198, 198, 198, 198, 198, 198, 198, 198, 198, 53, 53, 53, 1, 1, 1, 53, 53] 198 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082155 none CC(C)(C)OC(=O)N1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [28, 18, 28, 28, 7, 1, 7, 1, 1, 1, 1, 13, 13, 53, 53, 53, 53, 53, 53, 75, 75, 53, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 53, 53, 53, 1, 1] 198 rigid atoms, others: [32, 33, 34, 5, 38, 7, 8, 9, 10, 39, 22] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082155 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082155 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082155/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082155 Building REAL300000082156 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082156' /scratch/stefan/7930160/working/building/REAL300000082156 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082156 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082156/0 /scratch/stefan/7930160/working/building/REAL300000082156 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/166 `/scratch/stefan/7930160/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(Cl)=C2)=CC=C1F) `REAL300000082156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082156 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 55, 83, 55, 55, 24, 6, 6, 1, 1, 1, 1, 1, 1, 9, 37, 36, 1, 1, 1, 55, 55, 55, 55, 55, 24, 6, 1, 1, 37, 1, 55, 55] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 19, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 29, 31]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082156 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 21, 21, 55, 55, 43, 55, 153, 201, 201, 55, 55, 55, 1, 1, 1, 1, 1, 5, 21, 55, 55, 201, 55, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082156 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082156 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082156/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082156 Building REAL300000082157 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082157' /scratch/stefan/7930160/working/building/REAL300000082157 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082157 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082157/0 /scratch/stefan/7930160/working/building/REAL300000082157 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/167 `/scratch/stefan/7930160/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCS(=O)(=O)C2)=CC=C1F) `REAL300000082157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082157 none O=C([O-])C1=CC(N=NC2CCCS(=O)(=O)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 30, 31]) 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: REAL300000082157 none O=C([O-])C1=CC(N=NC2CCCS(=O)(=O)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 11, 11, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082157 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082157 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082157/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082157 Building REAL300000082158 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082158' /scratch/stefan/7930160/working/building/REAL300000082158 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082158 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082158/0 /scratch/stefan/7930160/working/building/REAL300000082158 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/168 `/scratch/stefan/7930160/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2CC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)C2)C=C1) `REAL300000082158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082158 none CC1=CC=C(C2CC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 7, 7, 1, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 47, 67, 67, 47, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 47, 47, 47, 1, 1, 7, 7] 96 rigid atoms, others: [35, 4, 5, 6, 7, 8, 20, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 37, 38]) total number of confs: 168 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: REAL300000082158 none CC1=CC=C(C2CC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 52, 52, 95, 95, 95, 95, 95, 95, 95, 95, 95, 8, 1, 1, 2, 2, 2, 1, 1, 8, 8, 8, 8, 95, 95, 95, 8, 8, 1, 1] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082158 none CC1=CC=C(C2CC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 73, 96, 96, 47, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 96, 96, 96, 96, 96, 96, 96, 47, 47, 47, 47, 1, 1, 1, 47, 47, 96, 96] 96 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 301 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082158 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082158 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082158/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082158 Building REAL300000082159 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082159' /scratch/stefan/7930160/working/building/REAL300000082159 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082159 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082159/0 /scratch/stefan/7930160/working/building/REAL300000082159 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/169 `/scratch/stefan/7930160/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082159 none COCCC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 75, 48, 28, 7, 28, 57, 90, 90, 90, 90, 90, 90, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 101, 101, 70, 75, 55, 55, 28, 57, 57, 90, 90, 90, 90, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082159 none COCCC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 40, 26, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 41, 41, 90, 90, 90, 90, 90, 90, 117, 117, 90, 77, 77, 77, 40, 40, 26, 26, 11, 3, 3, 1, 1, 1, 1, 90, 90, 90] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082159 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082159 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082159/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082159 Building REAL300000082160 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082160' /scratch/stefan/7930160/working/building/REAL300000082160 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082160 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082160/0 /scratch/stefan/7930160/working/building/REAL300000082160 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/170 `/scratch/stefan/7930160/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C2=CSC(C)=N2)=C1) `REAL300000082160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082160 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C2=CSC(C)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 12, 12, 51, 98, 98, 98, 98, 98, 98, 131, 131, 98, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 13, 13, 13, 51, 98, 98, 98, 1, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 1, 37, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 352 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082160 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C2=CSC(C)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 98, 98, 98, 98, 201, 201, 201, 201, 201, 98, 24, 24, 24, 5, 1, 1, 1, 98, 201, 201, 201, 201, 98] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082160 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C2=CSC(C)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 67, 67, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 67, 153, 201, 201, 201, 13, 1, 2, 2, 2, 13] 201 rigid atoms, others: [33, 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, 34, 35, 36, 37]) total number of confs: 472 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082160 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082160 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082160/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082160 Building REAL300000082161 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082161' /scratch/stefan/7930160/working/building/REAL300000082161 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082161 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082161/0 /scratch/stefan/7930160/working/building/REAL300000082161 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/171 `/scratch/stefan/7930160/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=C(C=CO2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082161 none CC1(C)CC2=C(C=CO2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 23, 23] 23 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 45 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: REAL300000082161 none CC1(C)CC2=C(C=CO2)C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 23, 23, 23, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 32, 22, 38, 29, 30, 31] set([33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 45 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082161 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082161 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082161/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082161 Building REAL300000082162 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082162' /scratch/stefan/7930160/working/building/REAL300000082162 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082162 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082162/0 /scratch/stefan/7930160/working/building/REAL300000082162 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/172 `/scratch/stefan/7930160/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082162 none CC(C)(C)OC(=O)NC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 169, 119, 169, 42, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 42, 42, 42, 42, 42, 42, 1, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [42, 43, 44, 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, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082162 none CC(C)(C)OC(=O)NC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 26, 26, 11, 6, 11, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 42, 42, 42, 42, 63, 63, 42, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 46, 47, 48, 40, 41, 24, 25, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082162 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082162 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082162/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082162 Building REAL300000082163 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082163' /scratch/stefan/7930160/working/building/REAL300000082163 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082163 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082163/0 /scratch/stefan/7930160/working/building/REAL300000082163 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/173 `/scratch/stefan/7930160/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(C)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082163 none CCC(CC1=CC=C(C)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 9, 66, 147, 169, 169, 158, 169, 169, 169, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 108, 108, 108, 66, 147, 147, 169, 169, 169, 169, 169, 169, 169, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37]) total number of confs: 1018 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: REAL300000082163 none CCC(CC1=CC=C(C)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 169, 169, 169, 169, 169, 169, 201, 201, 169, 18, 18, 18, 18, 18, 9, 4, 4, 1, 1, 2, 2, 2, 1, 1, 169, 169, 169] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 36, 37, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40]) total number of confs: 426 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082163 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082163 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082163/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082163 Building REAL300000082164 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082164' /scratch/stefan/7930160/working/building/REAL300000082164 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082164 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082164/0 /scratch/stefan/7930160/working/building/REAL300000082164 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/174 `/scratch/stefan/7930160/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CC2=CC=CC=C2)=CC=C1F) `REAL300000082164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082164 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 124, 172, 124, 124, 52, 52, 14, 4, 3, 1, 1, 1, 1, 1, 1, 1, 14, 34, 36, 36, 34, 36, 36, 124, 124, 124, 124, 124, 14, 4, 4, 3, 3, 1, 1, 1, 1, 1, 34, 34, 36, 36, 36, 36, 36, 124, 124] 201 rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082164 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 47, 91, 112, 124, 124, 116, 124, 124, 47, 118, 120, 120, 118, 120, 120, 1, 1, 1, 1, 1, 47, 102, 102, 108, 112, 124, 124, 124, 124, 124, 118, 118, 120, 120, 120, 120, 120, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082164 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 120, 140, 120, 120, 39, 39, 7, 2, 7, 22, 26, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 7, 22, 22, 26, 26, 36, 36, 36, 36, 36, 2, 2, 1, 1, 1, 1, 1, 120, 120] 201 rigid atoms, others: [41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082164 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082164 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082164/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082164 Building REAL300000082165 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082165' /scratch/stefan/7930160/working/building/REAL300000082165 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082165 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082165/0 /scratch/stefan/7930160/working/building/REAL300000082165 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/175 `/scratch/stefan/7930160/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CC2)=CC=C1F) `REAL300000082165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082165 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 175, 153, 154, 49, 49, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 154, 154, 154, 154, 154, 9, 3, 3, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 154, 154] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000082165 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 58, 129, 154, 154, 145, 154, 154, 58, 103, 103, 1, 1, 1, 1, 1, 58, 129, 129, 154, 154, 154, 154, 154, 103, 103, 103, 103, 103, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 744 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082165 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 103, 139, 103, 103, 31, 31, 9, 1, 9, 22, 26, 26, 24, 26, 26, 1, 1, 1, 103, 103, 103, 103, 103, 9, 22, 22, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 103, 103] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 374 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082165 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082165 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082165/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082165 Building REAL300000082166 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082166' /scratch/stefan/7930160/working/building/REAL300000082166 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082166 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082166/0 /scratch/stefan/7930160/working/building/REAL300000082166 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/176 `/scratch/stefan/7930160/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082166 none CC1=CC=CC=C1C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [7, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 53, 96, 96, 96, 96, 96, 96, 115, 115, 96, 1, 7, 7, 7, 7, 1, 7, 7, 1, 1, 1, 13, 53, 96, 96, 96, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 35, 41, 25] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082166 none CC1=CC=CC=C1C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 47, 47, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 47, 138, 201, 201, 201, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082166 none CC1=CC=CC=C1C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 96, 201, 201, 96, 96, 96, 96, 96, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 95, 201, 201, 201, 201, 96, 201, 201, 96, 96, 96, 33, 9, 1, 1, 1, 96] 201 rigid atoms, others: [38, 39, 40, 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, 41]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082166 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082166 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082166/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082166 Building REAL300000082167 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082167' /scratch/stefan/7930160/working/building/REAL300000082167 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082167 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082167/0 /scratch/stefan/7930160/working/building/REAL300000082167 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/177 `/scratch/stefan/7930160/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1) `REAL300000082167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082167 none COC1=CC=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need 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, 118, 118, 118, 118, 118, 40, 9, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 118, 118, 118, 201, 201, 201, 118, 118, 40, 40, 40, 40, 1, 1, 1, 118, 118, 118, 118] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 405 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: REAL300000082167 none COC1=CC=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 8, 8, 52, 52, 118, 118, 118, 118, 118, 118, 201, 201, 118, 1, 1, 1, 1, 3, 3, 3, 1, 1, 8, 8, 8, 8, 118, 118, 118, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 517 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082167 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082167/1 /scratch/stefan/7930160/working/building/REAL300000082167 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/178 `/scratch/stefan/7930160/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2OC(C(C)=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1) `REAL300000082167.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082167 none COC1=CC=C2OC(C(C)=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 133, 133, 133, 133, 133, 133, 56, 56, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 133, 168, 168, 168, 133, 133, 56, 56, 56, 13, 1, 1, 1, 133, 133, 133, 133] 168 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 279 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082167 none COC1=CC=C2OC(C(C)=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 133, 133, 133, 133, 133, 133, 168, 168, 133, 1, 1, 1, 1, 3, 3, 3, 1, 1, 12, 12, 12, 44, 133, 133, 133, 2, 2, 2, 1] 168 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 378 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082167 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082167 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082167/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082167/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082167 Building REAL300000082168 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082168' /scratch/stefan/7930160/working/building/REAL300000082168 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082168 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082168/0 /scratch/stefan/7930160/working/building/REAL300000082168 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/179 `/scratch/stefan/7930160/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(Cl)=C3Cl)=CC=C1F) `REAL300000082168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082168 none O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(Cl)=C3Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 38 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: REAL300000082168 none O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(Cl)=C3Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082168 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082168 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082168/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082168 Building REAL300000082169 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082169' /scratch/stefan/7930160/working/building/REAL300000082169 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082169 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082169/0 /scratch/stefan/7930160/working/building/REAL300000082169 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/180 `/scratch/stefan/7930160/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(NS(C)(=O)=O)=C1) `REAL300000082169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082169 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(NS(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 39, 73, 73, 73, 73, 73, 73, 91, 91, 73, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1, 11, 11, 11, 39, 73, 73, 73, 1, 1, 1, 7, 17, 17, 17, 1] 201 rigid atoms, others: [32, 1, 34, 33, 39, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) 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: REAL300000082169 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(NS(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 73, 73, 73, 73, 73, 175, 201, 201, 201, 73, 19, 19, 19, 5, 1, 1, 1, 73, 73, 73, 175, 201, 201, 201, 73] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 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: 568 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082169 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082169 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082169/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082169 Building REAL300000082170 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082170' /scratch/stefan/7930160/working/building/REAL300000082170 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082170 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082170/0 /scratch/stefan/7930160/working/building/REAL300000082170 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/181 `/scratch/stefan/7930160/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OC2=C(C=CC(Cl)=C2Cl)C1=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082170 none CC1OC2=C(C=CC(Cl)=C2Cl)C1=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1] 36 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 61 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: REAL300000082170 none CC1OC2=C(C=CC(Cl)=C2Cl)C1=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 1, 7, 36, 36, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 56 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082170 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082170 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082170/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082170 Building REAL300000082171 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082171' /scratch/stefan/7930160/working/building/REAL300000082171 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082171 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082171/0 /scratch/stefan/7930160/working/building/REAL300000082171 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/182 `/scratch/stefan/7930160/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=CS1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082171 none CCC(CC1=CC=CS1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 9, 43, 93, 155, 155, 155, 155, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 72, 72, 72, 72, 72, 43, 93, 93, 155, 155, 155, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 721 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: REAL300000082171 none CCC(CC1=CC=CS1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 1, 1, 1, 1, 1, 1, 13, 55, 55, 155, 155, 155, 155, 155, 155, 189, 189, 155, 20, 20, 20, 20, 20, 13, 4, 4, 1, 1, 1, 155, 155, 155] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 412 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082171 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082171 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082171/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082171 Building REAL300000082172 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082172' /scratch/stefan/7930160/working/building/REAL300000082172 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082172 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082172/0 /scratch/stefan/7930160/working/building/REAL300000082172 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/183 `/scratch/stefan/7930160/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1) `REAL300000082172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082172 none CC1(C)CC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 50, 12, 1, 1, 1, 117, 117] 117 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082172 none CC1(C)CC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 1, 10, 10, 50, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 10, 50, 117, 117, 117, 1, 1] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 20, 21, 22, 23, 39, 38, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082172 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082172 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082172/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082172 Building REAL300000082173 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082173' /scratch/stefan/7930160/working/building/REAL300000082173 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082173 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082173/0 /scratch/stefan/7930160/working/building/REAL300000082173 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/184 `/scratch/stefan/7930160/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCN1C(=O)C2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082173 none CC(CCN1C(=O)C2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 7, 47, 105, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 47, 47, 112, 112, 143, 136, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082173 none CC(CCN1C(=O)C2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 25, 24, 8, 8, 5, 5, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 38, 37] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082173 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082173 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082173/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082173 Building REAL300000082174 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082174' /scratch/stefan/7930160/working/building/REAL300000082174 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082174 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082174/0 /scratch/stefan/7930160/working/building/REAL300000082174 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/185 `/scratch/stefan/7930160/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082174 none CCC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 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: [65, 49, 9, 49, 108, 174, 174, 108, 155, 174, 174, 174, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 79, 79, 79, 49, 108, 108, 174, 174, 174, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 1078 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: REAL300000082174 none CCC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 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: [22, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 61, 61, 174, 174, 174, 174, 174, 174, 201, 201, 174, 22, 22, 22, 22, 22, 13, 6, 6, 1, 1, 1, 174, 174, 174] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 423 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082174 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082174 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082174/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082174 Building REAL300000082175 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082175' /scratch/stefan/7930160/working/building/REAL300000082175 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082175 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082175/0 /scratch/stefan/7930160/working/building/REAL300000082175 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/186 `/scratch/stefan/7930160/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082175 none CC(C)CC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 45, 9, 45, 106, 200, 200, 200, 200, 200, 200, 200, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 45, 106, 106, 200, 200, 200, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 662 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: REAL300000082175 none CC(C)CC(CC1=CC=C(Cl)C=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 70, 70, 200, 200, 200, 200, 200, 200, 201, 201, 200, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 7, 7, 1, 1, 1, 200, 200, 200] 201 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 40, 6] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 366 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082175 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082175 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082175/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082175 Building REAL300000082176 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082176' /scratch/stefan/7930160/working/building/REAL300000082176 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082176 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082176/0 /scratch/stefan/7930160/working/building/REAL300000082176 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/187 `/scratch/stefan/7930160/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2) `REAL300000082176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082176 none CC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 31, 31, 10, 1, 1, 1, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082176 none CC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 7, 31, 31, 31, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 19, 20, 21, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082176 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082176/1 /scratch/stefan/7930160/working/building/REAL300000082176 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/188 `/scratch/stefan/7930160/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2) `REAL300000082176.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082176 none CC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082176 none CC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 19, 20, 21, 25, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082176 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082176 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082176/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082176/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082176 Building REAL300000082177 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082177' /scratch/stefan/7930160/working/building/REAL300000082177 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082177 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082177/0 /scratch/stefan/7930160/working/building/REAL300000082177 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/189 `/scratch/stefan/7930160/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082177 none COC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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, 153, 153, 153, 153, 153, 153, 64, 64, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 153, 153, 201, 201, 201, 153, 153, 153, 153, 64, 13, 1, 1, 1, 153] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082177 none COC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60, 153, 153, 153, 153, 153, 153, 198, 198, 153, 1, 1, 3, 3, 3, 1, 1, 1, 1, 10, 60, 153, 153, 153, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 36, 27, 28, 29, 30] set([0, 32, 34, 35, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 31]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082177 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082177 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082177/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082177 Building REAL300000082178 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082178' /scratch/stefan/7930160/working/building/REAL300000082178 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082178 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082178/0 /scratch/stefan/7930160/working/building/REAL300000082178 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/190 `/scratch/stefan/7930160/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCOC1=CC=CC=C1C(N)=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082178 none CC(CCCOC1=CC=CC=C1C(N)=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 35, 38, 62, 156, 201, 201, 201, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 21, 21, 21, 35, 35, 38, 38, 62, 62, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082178 none CC(CCCOC1=CC=CC=C1C(N)=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 33, 26, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 63, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 63, 63, 63, 33, 32, 30, 30, 14, 14, 1, 1, 1, 1, 3, 3, 201, 201, 201] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082178 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082178 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082178/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082178 Building REAL300000082179 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082179' /scratch/stefan/7930160/working/building/REAL300000082179 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082179 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082179/0 /scratch/stefan/7930160/working/building/REAL300000082179 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/191 `/scratch/stefan/7930160/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC3=CC(Br)=CC=C3C2)=CC=C1F) `REAL300000082179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082179 none O=C([O-])C1=CC(N=NC2CCC3=CC(Br)=CC=C3C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 22, 23, 35]) 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: REAL300000082179 none O=C([O-])C1=CC(N=NC2CCC3=CC(Br)=CC=C3C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082179 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082179 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082179/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082179 Building REAL300000082180 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082180' /scratch/stefan/7930160/working/building/REAL300000082180 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082180 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082180/0 /scratch/stefan/7930160/working/building/REAL300000082180 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/192 `/scratch/stefan/7930160/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC(C)=C1) `REAL300000082180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082180 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 33, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 84, 84, 84, 1, 2, 2, 2, 1, 2, 2, 2, 1] 84 rigid atoms, others: [1, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36]) total number of confs: 170 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: REAL300000082180 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 84, 84, 84, 45, 84, 84, 84, 45, 45, 45, 10, 1, 1, 1, 84, 84, 84, 84, 45, 84, 84, 84, 84] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 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: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082180 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082180 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082180/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082180 Building REAL300000082181 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082181' /scratch/stefan/7930160/working/building/REAL300000082181 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082181 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082181/0 /scratch/stefan/7930160/working/building/REAL300000082181 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/193 `/scratch/stefan/7930160/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1OC) `REAL300000082181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082181 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [115, 75, 75, 75, 75, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 75, 110, 115, 115, 115, 75, 75, 32, 8, 1, 1, 1, 110, 110, 110] 116 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) 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: REAL300000082181 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 39, 75, 75, 75, 75, 75, 75, 96, 96, 75, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 39, 75, 75, 75, 4, 4, 4] 116 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082181 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082181 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082181/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082181 Building REAL300000082182 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082182' /scratch/stefan/7930160/working/building/REAL300000082182 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082182 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082182/0 /scratch/stefan/7930160/working/building/REAL300000082182 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/194 `/scratch/stefan/7930160/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=C(F)C(F)=C1) `REAL300000082182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082182 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 35, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 35, 89, 89, 89, 1, 1] 89 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 158 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082182 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 88, 88, 88, 79, 88, 88, 88, 88, 48, 48, 48, 10, 1, 1, 1, 88, 88] 88 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082182 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082182 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082182/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082182 Building REAL300000082183 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082183' /scratch/stefan/7930160/working/building/REAL300000082183 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082183 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082183/0 /scratch/stefan/7930160/working/building/REAL300000082183 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/195 `/scratch/stefan/7930160/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082183 none COCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 172, 109, 70, 28, 28, 38, 38, 19, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 201, 201, 201, 172, 172, 109, 109, 38, 37, 18, 4, 1, 1, 1, 38, 38] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 722 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: REAL300000082183 none COCCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 23, 9, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 37, 37, 37, 37, 37, 38, 54, 54, 37, 1, 1, 51, 51, 51, 23, 23, 9, 9, 1, 1, 6, 20, 37, 37, 37, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 39, 22, 23, 38, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 281 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082183 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082183 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082183/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082183 Building REAL300000082184 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082184' /scratch/stefan/7930160/working/building/REAL300000082184 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082184 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082184/0 /scratch/stefan/7930160/working/building/REAL300000082184 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/196 `/scratch/stefan/7930160/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082184 none CC(C)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 160, 201, 127, 59, 59, 86, 86, 35, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 159, 159, 86, 85, 34, 8, 1, 1, 1, 86, 86] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 752 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: REAL300000082184 none CC(C)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 17, 3, 1, 1, 1, 1, 1, 1, 6, 6, 41, 85, 85, 85, 85, 85, 86, 123, 123, 85, 1, 1, 17, 17, 17, 17, 17, 17, 17, 10, 10, 1, 1, 6, 41, 85, 85, 85, 1, 1] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 393 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082184 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082184 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082184/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082184 Building REAL300000082185 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082185' /scratch/stefan/7930160/working/building/REAL300000082185 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082185 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082185/0 /scratch/stefan/7930160/working/building/REAL300000082185 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/197 `/scratch/stefan/7930160/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=NC(C3=CC=CC=C3)=N2)=CC=C1F) `REAL300000082185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082185 none O=C([O-])C1=CC(NN=CC2=CC=NC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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] 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: [96, 78, 96, 78, 78, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 78, 78, 78, 78, 78, 23, 7, 1, 1, 6, 6, 1, 6, 6, 78, 78] 104 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300000082185 none O=C([O-])C1=CC(NN=CC2=CC=NC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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] 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: [3, 1, 3, 1, 1, 1, 1, 11, 55, 55, 78, 78, 78, 78, 78, 104, 104, 78, 104, 104, 78, 1, 1, 1, 1, 1, 11, 55, 78, 78, 104, 104, 78, 104, 104, 1, 1] 104 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082185 none O=C([O-])C1=CC(NN=CC2=CC=NC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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] 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, 54, 24, 24, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 104, 104, 104, 104, 104, 54, 24, 6, 6, 1, 1, 1, 1, 1, 104, 104] 104 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 205 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082185 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082185 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082185/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082185 Building REAL300000082186 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082186' /scratch/stefan/7930160/working/building/REAL300000082186 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082186 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082186/0 /scratch/stefan/7930160/working/building/REAL300000082186 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/198 `/scratch/stefan/7930160/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000082186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082186 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 142, 100, 142, 142, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 142, 142, 142, 142, 142, 201, 201, 201, 142, 142, 57, 11, 1, 1, 1, 142] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082186 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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: [4, 1, 1, 1, 1, 1, 1, 7, 7, 52, 142, 142, 141, 141, 142, 142, 201, 201, 142, 1, 1, 1, 2, 2, 4, 4, 4, 1, 1, 7, 52, 142, 142, 142, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 27, 28] set([0, 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: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082186 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082186 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082186/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082186 Building REAL300000082187 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082187' /scratch/stefan/7930160/working/building/REAL300000082187 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082187 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082187/0 /scratch/stefan/7930160/working/building/REAL300000082187 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/199 `/scratch/stefan/7930160/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082187 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 189, 201, 99, 40, 40, 40, 40, 40, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 189, 189, 40, 40, 40, 23, 7, 1, 1, 1, 40] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 593 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: REAL300000082187 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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: [43, 25, 43, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 40, 40, 40, 40, 40, 40, 62, 62, 40, 1, 25, 25, 1, 1, 1, 7, 18, 40, 40, 40, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 23, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 301 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082187 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082187 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082187/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082187 Building REAL300000082188 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082188' /scratch/stefan/7930160/working/building/REAL300000082188 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082188 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082188/0 /scratch/stefan/7930160/working/building/REAL300000082188 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/200 `/scratch/stefan/7930160/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2F)=CC=C1F) `REAL300000082188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082188 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 63, 64, 63, 63, 36, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 63, 63, 63, 63, 63, 36, 10, 1, 1, 1, 63, 63] 64 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082188 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 63, 63, 63, 64, 64, 64, 49, 63, 63, 63, 1, 1, 1, 1, 1, 10, 40, 63, 62, 63, 1, 1] 64 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082188 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082188 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082188/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082188 Building REAL300000082189 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082189' /scratch/stefan/7930160/working/building/REAL300000082189 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082189 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082189/0 /scratch/stefan/7930160/working/building/REAL300000082189 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/201 `/scratch/stefan/7930160/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082189 none N#CC1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 51, 51, 51, 51, 51, 51, 53, 53, 51, 1, 14, 14, 14, 14, 2, 2, 1, 1, 1, 6, 26, 51, 51, 51, 1] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 43, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082189 none N#CC1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 7, 7, 14, 14, 15, 15, 15, 79, 79, 136, 201, 201, 201, 200, 201, 201, 201, 201, 201, 15, 1, 1, 1, 1, 7, 7, 14, 14, 15, 79, 136, 201, 201, 201, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082189 none N#CC1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 79, 79, 51, 51, 51, 51, 51, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 201, 201, 201, 201, 79, 79, 51, 51, 51, 25, 7, 1, 1, 1, 51] 201 rigid atoms, others: [40, 41, 42, 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, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082189 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082189 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082189/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082189 Building REAL300000082190 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082190' /scratch/stefan/7930160/working/building/REAL300000082190 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082190 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082190/0 /scratch/stefan/7930160/working/building/REAL300000082190 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/202 `/scratch/stefan/7930160/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=NC3=CC=CC=C23)=CC=C1F) `REAL300000082190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082190 none O=C([O-])C1=CC(NN=CC2=CC=NC3=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 51, 9, 1, 1, 1, 1, 1, 1, 103, 103] 103 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082190 none O=C([O-])C1=CC(NN=CC2=CC=NC3=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 3, 1, 1, 1, 1, 13, 51, 51, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 13, 51, 103, 103, 103, 103, 103, 103, 1, 1] 103 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082190 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082190 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082190/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082190 Building REAL300000082191 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082191' /scratch/stefan/7930160/working/building/REAL300000082191 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082191 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082191/0 /scratch/stefan/7930160/working/building/REAL300000082191 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/203 `/scratch/stefan/7930160/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC1=CC=CN=C1) `REAL300000082191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082191 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 35, 39, 117, 201, 201, 201, 201, 201, 54, 54, 54, 54, 21, 7, 1, 1, 1, 54, 54, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082191 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 25, 54, 54, 54, 54, 54, 54, 58, 58, 54, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 2, 2, 2, 1, 7, 25, 54, 54, 54, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 17, 18, 19, 20, 36, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082191 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 78, 78, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 78, 132, 201, 201, 201, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 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: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082191 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082191 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082191/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082191 Building REAL300000082192 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082192' /scratch/stefan/7930160/working/building/REAL300000082192 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082192 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082192/0 /scratch/stefan/7930160/working/building/REAL300000082192 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/204 `/scratch/stefan/7930160/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082192 none COC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 181, 181, 125, 181, 181, 181, 58, 58, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 181, 181, 181, 58, 10, 1, 1, 1] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082192 none COC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 93, 181, 181, 181, 181, 181, 181, 201, 201, 181, 3, 3, 3, 1, 1, 1, 12, 93, 181, 181, 181] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082192 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082192 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082192/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082192 Building REAL300000082193 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082193' /scratch/stefan/7930160/working/building/REAL300000082193 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082193 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082193/0 /scratch/stefan/7930160/working/building/REAL300000082193 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/205 `/scratch/stefan/7930160/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1Cl) `REAL300000082193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082193 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [9, 1, 9, 9, 43, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 110, 110, 110, 1, 1, 1] 110 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 194 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082193 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 110, 110, 101, 110, 110, 110, 110, 55, 55, 55, 10, 1, 1, 1, 110, 110, 110] 110 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082193 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082193 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082193/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082193 Building REAL300000082194 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082194' /scratch/stefan/7930160/working/building/REAL300000082194 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082194 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082194/0 /scratch/stefan/7930160/working/building/REAL300000082194 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/206 `/scratch/stefan/7930160/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)C1=CC=C(F)C=C1) `REAL300000082194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082194 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 16, 57, 57, 128, 128, 128, 128, 128, 128, 128, 128, 128, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 128, 128, 128, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 128 rigid atoms, others: [37, 38, 39, 40, 14, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082194 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 109, 108, 116, 127, 127, 116, 126, 127, 127, 39, 39, 39, 39, 1, 1, 1, 116, 116, 116, 116, 116, 116, 127, 127, 127, 127] 127 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082194 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082194 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082194/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082194 Building REAL300000082195 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082195' /scratch/stefan/7930160/working/building/REAL300000082195 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082195 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082195/0 /scratch/stefan/7930160/working/building/REAL300000082195 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/207 `/scratch/stefan/7930160/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082195 none CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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 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, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 111, 111, 111, 111, 111, 111, 111, 111, 111, 51, 13, 1, 1, 1, 111] 111 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) 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: REAL300000082195 none CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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 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, 10, 10, 54, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 54, 111, 111, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 26, 27, 28, 29] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 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/7930160/working/building/REAL300000082195 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082195 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082195/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082195 Building REAL300000082196 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082196' /scratch/stefan/7930160/working/building/REAL300000082196 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082196 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082196/0 /scratch/stefan/7930160/working/building/REAL300000082196 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/208 `/scratch/stefan/7930160/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082196 none COC(=O)C1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 10, 16, 10, 10, 10, 10, 10, 10, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 10, 10, 16, 16, 16, 10, 10, 10, 10, 6, 4, 1, 1, 1, 10] 16 rigid atoms, others: [35, 36, 37, 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, 38]) 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: REAL300000082196 none COC(=O)C1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 15, 15, 10, 1, 1, 8, 8, 8, 1, 1, 1, 1, 3, 5, 10, 10, 10, 1] 16 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 38, 29, 30, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082196 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082196 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082196/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082196 Building REAL300000082197 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082197' /scratch/stefan/7930160/working/building/REAL300000082197 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082197 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082197/0 /scratch/stefan/7930160/working/building/REAL300000082197 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/209 `/scratch/stefan/7930160/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1) `REAL300000082197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082197 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 1, 12, 12, 54, 133, 133, 133, 133, 133, 133, 135, 135, 133, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 53, 133, 133, 132, 1, 1] 171 rigid atoms, others: [2, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 328 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082197 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [95, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 133, 132, 132, 132, 132, 95, 95, 95, 95, 95, 10, 1, 1, 1, 133, 133] 171 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 445 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082197 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082197 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082197/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082197 Building REAL300000082198 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082198' /scratch/stefan/7930160/working/building/REAL300000082198 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082198 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082198/0 /scratch/stefan/7930160/working/building/REAL300000082198 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/210 `/scratch/stefan/7930160/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082198 none C#CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 155, 70, 47, 109, 109, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 109, 109, 201, 201, 201, 109, 109, 25, 25, 25, 6, 1, 1, 1, 109, 109] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 702 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082198 none C#CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [11, 11, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 49, 109, 109, 109, 109, 109, 109, 140, 140, 109, 1, 1, 11, 12, 12, 1, 1, 13, 13, 13, 49, 109, 109, 109, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 36, 27, 28, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 370 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082198 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082198 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082198/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082198 Building REAL300000082199 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082199' /scratch/stefan/7930160/working/building/REAL300000082199 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082199 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082199/0 /scratch/stefan/7930160/working/building/REAL300000082199 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/211 `/scratch/stefan/7930160/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC[NH+](CCN3CCOCC3)CC2)=CC=C1F) `REAL300000082199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082199 none O=C([O-])C1=CC(N=NC2CC[NH+](CCN3CCOCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [59, 52, 59, 52, 52, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 10, 1, 1, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 3, 3, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 52, 52] 105 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 46, 45, 48, 21, 22, 47, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 123 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: REAL300000082199 none O=C([O-])C1=CC(N=NC2CC[NH+](CCN3CCOCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 52, 52, 52, 52, 52, 81, 97, 105, 105, 105, 105, 105, 52, 52, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 81, 81, 97, 97, 105, 105, 105, 105, 105, 105, 105, 105, 52, 52, 52, 52, 1, 1] 105 rigid atoms, others: [1, 3, 4, 5, 6, 49, 50, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 399 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082199 none O=C([O-])C1=CC(N=NC2CC[NH+](CCN3CCOCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 54, 54, 10, 10, 10, 10, 8, 10, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 105, 105, 105, 105, 105, 10, 10, 10, 10, 10, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 105, 105] 105 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082199 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082199 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082199/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082199 Building REAL300000082200 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082200' /scratch/stefan/7930160/working/building/REAL300000082200 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082200 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082200/0 /scratch/stefan/7930160/working/building/REAL300000082200 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/212 `/scratch/stefan/7930160/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)CC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082200 none CC1=CC=C(S(=O)(=O)CC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 88, 201, 201, 52, 8, 52, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 88, 88, 52, 52, 52, 52, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 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, 35, 39, 40]) total number of confs: 831 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082200 none CC1=CC=C(S(=O)(=O)CC(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 8, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 8, 22, 22, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 8, 22, 22, 22, 22, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 23, 24, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082200 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082200 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082200/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082200 Building REAL300000082201 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082201' /scratch/stefan/7930160/working/building/REAL300000082201 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082201 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082201/0 /scratch/stefan/7930160/working/building/REAL300000082201 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/213 `/scratch/stefan/7930160/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1) `REAL300000082201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082201 none CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 6, 11, 11, 6, 1, 6, 6, 17, 39, 39, 39, 39, 39, 39, 40, 40, 39, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 17, 39, 39, 39, 1, 1, 1, 1] 40 rigid atoms, others: [5, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 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: REAL300000082201 none CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 40, 40, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 39, 39, 25, 25, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 34, 34, 8, 1, 1, 1, 39, 39, 39, 39] 40 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082201 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082201 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082201/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082201 Building REAL300000082202 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082202' /scratch/stefan/7930160/working/building/REAL300000082202 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082202 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082202/0 /scratch/stefan/7930160/working/building/REAL300000082202 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/214 `/scratch/stefan/7930160/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CSC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082202 none CCC(CSC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 42, 8, 42, 85, 158, 194, 194, 189, 194, 194, 194, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 58, 58, 58, 58, 42, 85, 85, 194, 194, 194, 194, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 684 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: REAL300000082202 none CCC(CSC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 41, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 42, 119, 119, 194, 194, 194, 194, 194, 194, 201, 201, 194, 50, 50, 50, 50, 50, 42, 18, 18, 1, 1, 1, 1, 194, 194, 194] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 482 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082202 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082202 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082202/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082202 Building REAL300000082203 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082203' /scratch/stefan/7930160/working/building/REAL300000082203 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082203 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082203/0 /scratch/stefan/7930160/working/building/REAL300000082203 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/215 `/scratch/stefan/7930160/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F) `REAL300000082203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082203 none COC1=CC=C(C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [24, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 32, 56, 56, 32, 11, 11, 11, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 11] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45]) 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: REAL300000082203 none COC1=CC=C(C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 38, 38, 133, 133, 133, 133, 133, 133, 201, 201, 133, 1, 1, 1, 4, 4, 4, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 133, 133, 133, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 24, 25, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082203 none COC1=CC=C(C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 133, 133, 133, 133, 32, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 201, 201, 201, 133, 133, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 133] 201 rigid atoms, others: [42, 43, 44, 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, 38, 39, 40, 41, 45]) total number of confs: 342 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082203 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082203 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082203/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082203 Building REAL300000082204 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082204' /scratch/stefan/7930160/working/building/REAL300000082204 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082204 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082204/0 /scratch/stefan/7930160/working/building/REAL300000082204 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/216 `/scratch/stefan/7930160/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082204 none COC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [86, 63, 63, 63, 63, 63, 63, 121, 189, 189, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 86, 86, 86, 63, 63, 189, 19, 6, 1, 1, 1, 63] 201 rigid atoms, others: [33, 34, 35, 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, 36]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082204 none COC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 7, 40, 40, 1, 1, 12, 12, 28, 63, 63, 63, 63, 63, 63, 87, 87, 63, 1, 3, 3, 3, 1, 1, 40, 12, 28, 63, 63, 63, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 24, 36, 28, 29] set([0, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082204 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082204 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082204/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082204 Building REAL300000082205 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082205' /scratch/stefan/7930160/working/building/REAL300000082205 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082205 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082205/0 /scratch/stefan/7930160/working/building/REAL300000082205 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/217 `/scratch/stefan/7930160/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C(C)=C1) `REAL300000082205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082205 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 161, 161, 161, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 161, 161, 161, 1, 1, 2, 2, 2, 1] 161 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 293 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: REAL300000082205 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [53, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 161, 161, 54, 54, 161, 161, 161, 54, 54, 54, 11, 1, 1, 1, 161, 161, 161, 161, 161, 161] 161 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 434 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082205 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082205 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082205/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082205 Building REAL300000082206 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082206' /scratch/stefan/7930160/working/building/REAL300000082206 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082206 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082206/0 /scratch/stefan/7930160/working/building/REAL300000082206 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/218 `/scratch/stefan/7930160/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OC(F)(F)F)=C1) `REAL300000082206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082206 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 1, 10, 10, 36, 65, 65, 65, 65, 65, 65, 84, 84, 65, 1, 1, 1, 1, 1, 1, 12, 20, 20, 20, 1, 10, 10, 10, 36, 65, 65, 65, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 267 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082206 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 65, 65, 65, 65, 65, 201, 201, 201, 201, 65, 13, 13, 13, 4, 1, 1, 1, 65, 65, 65, 65] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082206 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082206 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082206/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082206 Building REAL300000082207 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082207' /scratch/stefan/7930160/working/building/REAL300000082207 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082207 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082207/0 /scratch/stefan/7930160/working/building/REAL300000082207 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/219 `/scratch/stefan/7930160/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)(F)F) `REAL300000082207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082207 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 89, 89, 89, 89, 89, 89, 127, 127, 89, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 9, 9, 9, 41, 89, 89, 89, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 375 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082207 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7] 0 hydrogens 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, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 89, 89, 89, 89, 89, 89, 197, 201, 201, 201, 25, 25, 25, 5, 1, 1, 1, 89, 89, 89, 89] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 325 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082207 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082207 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082207/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082207 Building REAL300000082208 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082208' /scratch/stefan/7930160/working/building/REAL300000082208 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082208 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082208/0 /scratch/stefan/7930160/working/building/REAL300000082208 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/220 `/scratch/stefan/7930160/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC(=O)[O-])=C1) `REAL300000082208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082208 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC(=O)[O-])=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [47, 34, 22, 34, 34, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 99, 177, 189, 189, 34, 47, 47, 47, 34, 34, 22, 9, 1, 1, 1, 177, 177, 34] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) 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: REAL300000082208 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC(=O)[O-])=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 4, 13, 34, 34, 34, 34, 34, 34, 51, 51, 34, 1, 1, 9, 38, 66, 66, 1, 3, 3, 3, 1, 1, 4, 13, 34, 34, 34, 38, 38, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 25, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 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/7930160/working/building/REAL300000082208 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082208 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082208/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082208 Building REAL300000082209 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082209' /scratch/stefan/7930160/working/building/REAL300000082209 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082209 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082209/0 /scratch/stefan/7930160/working/building/REAL300000082209 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/221 `/scratch/stefan/7930160/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082209 none COC1=CC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 107, 107, 107, 107, 107, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 107, 107, 107, 173, 187, 187, 187, 107, 107, 107, 107, 41, 41, 41, 10, 1, 1, 1, 107, 173, 173, 173] 201 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 428 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082209 none COC1=CC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 107, 107, 107, 107, 107, 107, 157, 157, 107, 1, 1, 1, 3, 4, 4, 4, 1, 2, 2, 2, 5, 5, 5, 27, 107, 107, 107, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 374 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082209 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082209 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082209/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082209 Building REAL300000082210 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082210' /scratch/stefan/7930160/working/building/REAL300000082210 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082210 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082210/0 /scratch/stefan/7930160/working/building/REAL300000082210 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/222 `/scratch/stefan/7930160/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1C) `REAL300000082210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082210 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [9, 1, 9, 9, 43, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 107, 107, 107, 1, 1, 1, 2, 2, 2] 107 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 201 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082210 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 107, 107, 73, 75, 107, 107, 107, 49, 49, 49, 11, 1, 1, 1, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 258 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082210 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082210 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082210/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082210 Building REAL300000082211 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082211' /scratch/stefan/7930160/working/building/REAL300000082211 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082211 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082211/0 /scratch/stefan/7930160/working/building/REAL300000082211 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/223 `/scratch/stefan/7930160/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082211 none COC1=CC=CC=C1C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 58, 138, 138, 138, 138, 138, 138, 164, 164, 138, 1, 1, 8, 8, 8, 4, 4, 4, 4, 1, 1, 13, 13, 13, 58, 138, 138, 138, 1, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 44, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082211 none COC1=CC=CC=C1C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 24, 24, 24, 91, 194, 194, 194, 194, 194, 194, 201, 201, 194, 4, 4, 3, 3, 3, 1, 1, 1, 1, 4, 4, 24, 24, 24, 91, 194, 194, 194, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 418 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082211 none COC1=CC=CC=C1C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 142, 194, 194, 52, 53, 138, 138, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 138, 138, 201, 201, 201, 194, 194, 194, 194, 138, 138, 32, 32, 32, 8, 1, 1, 1, 138, 138] 201 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45]) total number of confs: 759 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082211 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082211 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082211/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082211 Building REAL300000082212 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082212' /scratch/stefan/7930160/working/building/REAL300000082212 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082212 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082212/0 /scratch/stefan/7930160/working/building/REAL300000082212 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/224 `/scratch/stefan/7930160/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082212 none CC(CCC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 48, 132, 144, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 140, 140, 141, 144, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [37, 38, 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, 36]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082212 none CC(CCC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 21, 104, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 5, 5, 4, 4, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082212 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082212 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082212/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082212 Building REAL300000082213 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082213' /scratch/stefan/7930160/working/building/REAL300000082213 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082213 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082213/0 /scratch/stefan/7930160/working/building/REAL300000082213 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/225 `/scratch/stefan/7930160/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C2=CC=NC=C2)=C1) `REAL300000082213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082213 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C2=CC=NC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 57, 147, 147, 147, 147, 147, 147, 201, 201, 147, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 11, 11, 11, 57, 147, 147, 147, 1, 1, 1, 3, 3, 3, 3, 1] 201 rigid atoms, others: [1, 34, 35, 33, 40, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082213 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C2=CC=NC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 147, 31, 31, 31, 7, 1, 1, 1, 147, 147, 147, 201, 201, 201, 201, 147] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 312 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082213 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C2=CC=NC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens 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, 3, 21, 21, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 95, 201, 201, 201, 3, 3, 3, 1, 1, 1, 1, 3] 201 rigid atoms, others: [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, 35, 40]) total number of confs: 390 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082213 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082213 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082213/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082213 Building REAL300000082214 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082214' /scratch/stefan/7930160/working/building/REAL300000082214 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082214 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082214/0 /scratch/stefan/7930160/working/building/REAL300000082214 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/226 `/scratch/stefan/7930160/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C)C=C1) `REAL300000082214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082214 none CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 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: [102, 94, 102, 102, 88, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 117, 116, 102, 102, 102, 102, 102, 102, 102, 88, 88, 47, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 102, 102] 150 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 761 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: REAL300000082214 none CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 10, 39, 39, 108, 108, 108, 108, 108, 108, 133, 133, 108, 9, 28, 28, 1, 1, 2, 2, 2, 1, 1, 5, 5, 10, 108, 108, 108, 28, 28, 28, 28, 28, 28, 28, 1, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 353 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082214 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082214 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082214/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082214 Building REAL300000082215 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082215' /scratch/stefan/7930160/working/building/REAL300000082215 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082215 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082215/0 /scratch/stefan/7930160/working/building/REAL300000082215 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/227 `/scratch/stefan/7930160/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(=O)N2) `REAL300000082215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082215 none CC1=CC=C(F)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 32, 33, 33, 33, 32, 32, 12, 1, 1, 1, 32] 33 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082215 none CC1=CC=C(F)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 32, 32, 32, 33, 33, 32, 1, 1, 1, 2, 2, 2, 1, 1, 7, 32, 32, 32, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 33, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082215 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082215 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082215/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082215 Building REAL300000082216 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082216' /scratch/stefan/7930160/working/building/REAL300000082216 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082216 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082216/0 /scratch/stefan/7930160/working/building/REAL300000082216 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/228 `/scratch/stefan/7930160/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2[O-])=CC=C1F) `REAL300000082216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082216 none O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 16, 4, 1, 1, 1, 27, 27] 27 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082216 none O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 18, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 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/7930160/working/building/REAL300000082216 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082216 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082216/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082216 Building REAL300000082217 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082217' /scratch/stefan/7930160/working/building/REAL300000082217 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082217 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082217/0 /scratch/stefan/7930160/working/building/REAL300000082217 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/229 `/scratch/stefan/7930160/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082217 none CC(CC1=CC=CC=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [53, 9, 53, 107, 201, 201, 169, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 53, 53, 53, 107, 107, 201, 201, 172, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082217 none CC(CC1=CC=CC=C1Cl)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082217 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082217 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082217/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082217 Building REAL300000082218 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082218' /scratch/stefan/7930160/working/building/REAL300000082218 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082218 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082218/0 /scratch/stefan/7930160/working/building/REAL300000082218 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/230 `/scratch/stefan/7930160/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C)N=C1C) `REAL300000082218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082218 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [32, 12, 1, 12, 12, 60, 156, 156, 156, 156, 156, 156, 162, 162, 156, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 60, 156, 156, 156, 2, 2, 2, 2, 2, 2, 2, 2, 2] 169 rigid atoms, others: [2, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 408 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: REAL300000082218 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [104, 42, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 156, 156, 156, 156, 156, 156, 156, 104, 104, 104, 104, 104, 9, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156] 169 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 498 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082218 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082218 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082218/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082218 Building REAL300000082219 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082219' /scratch/stefan/7930160/working/building/REAL300000082219 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082219 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082219/0 /scratch/stefan/7930160/working/building/REAL300000082219 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/231 `/scratch/stefan/7930160/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2SC=CN21) `REAL300000082219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082219 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2SC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 1, 14, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 1, 10, 10, 62, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 141, 141, 141, 1, 1] 141 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082219 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2SC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 1, 14, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [59, 60, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 141, 141, 141, 141, 141, 141, 141, 140, 60, 60, 60, 11, 1, 1, 1, 141, 141] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082219 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082219 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082219/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082219 Building REAL300000082220 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082220' /scratch/stefan/7930160/working/building/REAL300000082220 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082220 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082220/0 /scratch/stefan/7930160/working/building/REAL300000082220 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/232 `/scratch/stefan/7930160/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082220 none CC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 33, 37, 37, 33, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 4, 4] 48 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 32, 36, 33, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41]) total number of confs: 79 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: REAL300000082220 none CC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 49, 49, 49, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082220 none CC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 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, 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: [33, 33, 48, 48, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 48, 48, 48, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 48, 48] 48 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 246 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082220 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082220 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082220/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082220 Building REAL300000082221 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082221' /scratch/stefan/7930160/working/building/REAL300000082221 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082221 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082221/0 /scratch/stefan/7930160/working/building/REAL300000082221 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/233 `/scratch/stefan/7930160/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)C=C1) `REAL300000082221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082221 none CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 147, 60, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 108, 108, 168, 168, 168, 168, 168, 168, 168, 147, 147, 60, 1, 1, 1, 108, 108, 108, 108, 108, 168, 168] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082221 none CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 73, 73, 187, 187, 187, 187, 186, 187, 194, 194, 187, 12, 31, 31, 1, 1, 2, 2, 2, 1, 1, 5, 5, 13, 187, 187, 187, 31, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082221 none CC1=CC=C(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 21, 8, 1, 8, 33, 33, 108, 108, 108, 108, 108, 108, 149, 149, 108, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 21, 21, 8, 108, 108, 108, 1, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [35, 36, 37, 6, 39, 19, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082221 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082221 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082221/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082221 Building REAL300000082222 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082222' /scratch/stefan/7930160/working/building/REAL300000082222 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082222 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082222/0 /scratch/stefan/7930160/working/building/REAL300000082222 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/234 `/scratch/stefan/7930160/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082222 none COC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 43, 43, 43, 43, 43, 43, 43, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 63, 63, 63, 43, 43, 43, 43, 43, 43, 43, 43, 10, 1, 1, 1, 43] 63 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 110 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: REAL300000082222 none COC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 63, 63, 43, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 1] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 39] set([0, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082222 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082222 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082222/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082222 Building REAL300000082223 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082223' /scratch/stefan/7930160/working/building/REAL300000082223 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082223 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082223/0 /scratch/stefan/7930160/working/building/REAL300000082223 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/235 `/scratch/stefan/7930160/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082223 none CC(C)(C)OC(=O)NCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 195, 155, 195, 61, 24, 24, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 61, 61, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1] 201 rigid atoms, others: [48, 46, 15, 16, 17, 18, 19, 20, 21, 22, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082223 none CC(C)(C)OC(=O)NCC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 45, 45, 40, 27, 40, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24, 24, 34, 34, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24] 201 rigid atoms, others: [45, 43, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082223 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082223 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082223/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082223 Building REAL300000082224 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082224' /scratch/stefan/7930160/working/building/REAL300000082224 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082224 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082224/0 /scratch/stefan/7930160/working/building/REAL300000082224 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/236 `/scratch/stefan/7930160/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C1=NC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CS1)C1CC1) `REAL300000082224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082224 none CC(=O)N(C1=NC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [149, 77, 149, 46, 46, 46, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 77, 126, 126, 149, 149, 149, 36, 9, 1, 1, 1, 46, 126, 126, 126, 126, 126] 159 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, 35, 36, 37, 38]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082224 none CC(=O)N(C1=NC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 1, 1, 1, 1, 1, 6, 6, 19, 46, 46, 45, 45, 46, 46, 56, 56, 46, 1, 1, 4, 8, 8, 10, 10, 10, 6, 19, 46, 46, 46, 1, 8, 8, 8, 8, 8] 159 rigid atoms, others: [33, 3, 4, 5, 6, 7, 20, 21] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082224 none CC(=O)N(C1=NC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 5, 8, 8, 8, 20, 20, 60, 126, 126, 126, 126, 126, 126, 137, 137, 126, 8, 8, 1, 1, 1, 11, 11, 11, 20, 60, 126, 126, 126, 8, 1, 1, 1, 1, 1] 159 rigid atoms, others: [34, 35, 36, 37, 38, 3, 22, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 306 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082224 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082224 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082224/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082224 Building REAL300000082225 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082225' /scratch/stefan/7930160/working/building/REAL300000082225 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082225 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082225/0 /scratch/stefan/7930160/working/building/REAL300000082225 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/237 `/scratch/stefan/7930160/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1) `REAL300000082225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082225 none CC1=CC(F)=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 10, 1, 1, 10, 10, 1, 1, 1, 1, 1, 1, 8, 8, 39, 76, 76, 75, 75, 76, 76, 104, 104, 76, 1, 10, 10, 10, 10, 10, 10, 1, 1, 8, 39, 76, 76, 76] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) 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: REAL300000082225 none CC1=CC(F)=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 58, 58, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 10, 2, 2, 2, 1, 1, 1, 10, 10, 58, 152, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082225 none CC1=CC(F)=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 201, 201, 119, 157, 201, 201, 76, 76, 76, 76, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 76, 201, 201, 201, 201, 201, 201, 76, 76, 33, 9, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082225 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082225 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082225/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082225 Building REAL300000082226 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082226' /scratch/stefan/7930160/working/building/REAL300000082226 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082226 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082226/0 /scratch/stefan/7930160/working/building/REAL300000082226 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/238 `/scratch/stefan/7930160/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)F)C=C2)=CC=C1F) `REAL300000082226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082226 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [67, 43, 67, 43, 43, 19, 5, 5, 1, 1, 1, 1, 1, 1, 6, 24, 63, 63, 1, 1, 43, 43, 43, 43, 43, 19, 5, 1, 1, 24, 24, 63, 1, 1, 43, 43] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35]) total number of confs: 413 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: REAL300000082226 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 25, 25, 43, 43, 25, 43, 124, 175, 201, 201, 43, 43, 1, 1, 1, 1, 1, 7, 25, 43, 43, 175, 175, 201, 43, 43, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 662 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082226 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082226 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082226/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082226 Building REAL300000082227 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082227' /scratch/stefan/7930160/working/building/REAL300000082227 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082227 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082227/0 /scratch/stefan/7930160/working/building/REAL300000082227 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/239 `/scratch/stefan/7930160/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(Br)C=C23)=CC=C1F) `REAL300000082227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082227 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 40, 40] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 60 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: REAL300000082227 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 40, 40, 1, 1] 40 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082227 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082227 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082227/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082227 Building REAL300000082228 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082228' /scratch/stefan/7930160/working/building/REAL300000082228 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082228 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082228/0 /scratch/stefan/7930160/working/building/REAL300000082228 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/240 `/scratch/stefan/7930160/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCCC3=CC=C(Cl)C=C32)=CC=C1F) `REAL300000082228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082228 none O=C([O-])C1=CC(NN=C2CCCCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 42, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 42 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 25, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082228 none O=C([O-])C1=CC(NN=C2CCCCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1] 42 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082228 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082228 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082228/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082228 Building REAL300000082229 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082229' /scratch/stefan/7930160/working/building/REAL300000082229 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082229 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082229/0 /scratch/stefan/7930160/working/building/REAL300000082229 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/241 `/scratch/stefan/7930160/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082229 none CCC(C)CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 189, 162, 189, 93, 72, 93, 72, 72, 38, 72, 72, 72, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 189, 189, 189, 189, 162, 162, 93, 93, 93, 72, 69, 72, 38, 9, 1, 1, 1] 201 rigid atoms, others: [48, 46, 47, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 858 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: REAL300000082229 none CCC(C)CN(C)C1=CC=C(F)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 19, 9, 19, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 72, 72, 72, 72, 72, 72, 108, 108, 72, 30, 30, 30, 30, 30, 19, 19, 19, 19, 9, 9, 4, 4, 4, 1, 1, 1, 6, 30, 72, 72, 72] 201 rigid atoms, others: [43, 5, 7, 8, 9, 10, 11, 12, 13, 14, 41, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 403 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082229 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082229 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082229/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082229 Building REAL300000082230 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082230' /scratch/stefan/7930160/working/building/REAL300000082230 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082230 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082230/0 /scratch/stefan/7930160/working/building/REAL300000082230 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/242 `/scratch/stefan/7930160/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(O)(C(F)(F)F)CC2)=CC=C1F) `REAL300000082230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082230 none O=C([O-])C1=CC(N=NC2CCC(O)(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 25, 25] 75 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 17, 18, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 34, 14, 15, 16, 19, 20, 21, 22, 23, 29, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082230 none O=C([O-])C1=CC(N=NC2CCC(O)(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 75, 25, 25, 25, 25, 1, 1] 75 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082230 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082230 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082230/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082230 Building REAL300000082231 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082231' /scratch/stefan/7930160/working/building/REAL300000082231 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082231 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082231/0 /scratch/stefan/7930160/working/building/REAL300000082231 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/243 `/scratch/stefan/7930160/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1) `REAL300000082231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082231 none COCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [85, 41, 21, 7, 1, 7, 7, 42, 102, 102, 102, 102, 102, 102, 139, 139, 102, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 41, 41, 21, 21, 42, 102, 102, 102, 1, 1, 1, 1] 201 rigid atoms, others: [35, 4, 37, 38, 17, 18, 19, 20, 21, 22, 23, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 561 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: REAL300000082231 none COCCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 117, 66, 29, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 102, 102, 30, 30, 102, 102, 166, 166, 166, 117, 117, 66, 66, 9, 1, 1, 1, 102, 102, 102, 102] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 798 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082231 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082231 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082231/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082231 Building REAL300000082232 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082232' /scratch/stefan/7930160/working/building/REAL300000082232 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082232 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082232/0 /scratch/stefan/7930160/working/building/REAL300000082232 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/244 `/scratch/stefan/7930160/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC(F)F)=CC=C1F) `REAL300000082232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082232 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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: [119, 88, 119, 88, 88, 52, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 39, 39, 88, 88, 88, 88, 88, 52, 10, 1, 1, 1, 39, 88, 88] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082232 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 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, 3, 1, 1, 1, 1, 4, 19, 19, 88, 88, 88, 45, 88, 88, 88, 170, 201, 201, 1, 1, 1, 1, 1, 4, 19, 88, 88, 88, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082232 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082232 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082232/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082232 Building REAL300000082233 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082233' /scratch/stefan/7930160/working/building/REAL300000082233 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082233 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082233/0 /scratch/stefan/7930160/working/building/REAL300000082233 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/245 `/scratch/stefan/7930160/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Br)C=CO2)=CC=C1F) `REAL300000082233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082233 none O=C([O-])C1=CC(NN=CC2=C(Br)C=CO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', '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, 8, 8, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 51, 8, 1, 1, 101, 101] 101 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 24, 25]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082233 none O=C([O-])C1=CC(NN=CC2=C(Br)C=CO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', '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, 8, 8, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 51, 51, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 13, 51, 101, 101, 1, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082233 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082233 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082233/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082233 Building REAL300000082234 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082234' /scratch/stefan/7930160/working/building/REAL300000082234 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082234 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082234/0 /scratch/stefan/7930160/working/building/REAL300000082234 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/246 `/scratch/stefan/7930160/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(F)F)C=C1) `REAL300000082234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082234 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [5, 1, 5, 5, 25, 51, 51, 51, 51, 51, 51, 76, 76, 51, 1, 1, 1, 1, 1, 11, 40, 40, 1, 1, 5, 5, 5, 25, 51, 51, 51, 1, 1, 40, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 322 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082234 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 51, 51, 23, 46, 172, 201, 201, 51, 51, 21, 21, 21, 4, 1, 1, 1, 51, 51, 198, 51, 51] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 515 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082234 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082234 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082234/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082234 Building REAL300000082235 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082235' /scratch/stefan/7930160/working/building/REAL300000082235 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082235 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082235/0 /scratch/stefan/7930160/working/building/REAL300000082235 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/247 `/scratch/stefan/7930160/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)C(F)F)C=C1) `REAL300000082235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082235 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)C(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 32, 99, 99, 99, 99, 99, 99, 141, 141, 99, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 1, 1, 6, 6, 6, 32, 99, 99, 99, 1, 1, 18, 1, 1] 201 rigid atoms, others: [1, 34, 36, 37, 33, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 392 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082235 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)C(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 99, 99, 41, 99, 143, 143, 143, 201, 201, 99, 99, 35, 35, 35, 8, 1, 1, 1, 99, 99, 201, 99, 99] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 966 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082235 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082235 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082235/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082235 Building REAL300000082236 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082236' /scratch/stefan/7930160/working/building/REAL300000082236 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082236 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082236/0 /scratch/stefan/7930160/working/building/REAL300000082236 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/248 `/scratch/stefan/7930160/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=CC=C1F) `REAL300000082236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082236 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 53, 64, 53, 53, 19, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 53, 53, 53, 53, 53, 19, 7, 1, 1, 7, 1, 7, 53, 53] 109 rigid atoms, others: [8, 9, 10, 11, 12, 13, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) 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: REAL300000082236 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 39, 39, 53, 53, 53, 53, 109, 109, 109, 54, 109, 109, 109, 53, 1, 1, 1, 1, 1, 9, 39, 53, 53, 109, 57, 109, 1, 1] 109 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082236 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 129, 39, 39, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 201, 201, 129, 39, 11, 11, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 430 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082236 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082236 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082236/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082236 Building REAL300000082237 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082237' /scratch/stefan/7930160/working/building/REAL300000082237 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082237 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082237/0 /scratch/stefan/7930160/working/building/REAL300000082237 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/249 `/scratch/stefan/7930160/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082237 none CCC1=NN(C)C(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 95, 95, 95, 95, 95, 95, 95, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 144, 144, 144, 144, 144, 95, 95, 95, 35, 9, 1, 1, 1] 144 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082237 none CCC1=NN(C)C(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 95, 95, 95, 95, 95, 95, 121, 121, 95, 5, 5, 5, 5, 5, 2, 2, 2, 11, 50, 95, 95, 95] 144 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082237 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082237 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082237/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082237 Building REAL300000082238 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082238' /scratch/stefan/7930160/working/building/REAL300000082238 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082238 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082238/0 /scratch/stefan/7930160/working/building/REAL300000082238 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/250 `/scratch/stefan/7930160/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C2=CC=CC=C2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl) `REAL300000082238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082238 none CN1N=C(C2=CC=CC=C2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 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, 7, 7, 7, 4, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 71, 120, 120, 120, 120, 120, 120, 120, 120, 120, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 28, 71, 120, 120, 120] 120 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) 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: REAL300000082238 none CN1N=C(C2=CC=CC=C2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 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, 7, 7, 7, 4, 7, 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 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, 6, 6, 2, 6, 6, 1, 1, 11, 11, 43, 110, 110, 109, 109, 110, 110, 118, 118, 110, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 11, 43, 110, 110, 110] 120 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 24, 25] set([5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082238 none CN1N=C(C2=CC=CC=C2)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 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, 7, 7, 7, 4, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 120, 120, 120, 120, 120, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 110, 110, 110, 110, 110, 120, 120, 120, 120, 120, 27, 9, 1, 1, 1] 120 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082238 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082238 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082238/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082238 Building REAL300000082239 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082239' /scratch/stefan/7930160/working/building/REAL300000082239 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082239 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082239/0 /scratch/stefan/7930160/working/building/REAL300000082239 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/251 `/scratch/stefan/7930160/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F) `REAL300000082239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082239 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 41, 71, 41, 41, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 13, 1, 41, 41, 41, 41, 41, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 41, 41] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082239 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 201, 201, 60, 201, 201, 201, 41, 1, 1, 1, 1, 1, 10, 41, 41, 41, 41, 41, 41, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082239 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 69, 13, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 69, 12, 12, 12, 12, 13, 13, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082239 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082239/1 /scratch/stefan/7930160/working/building/REAL300000082239 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/252 `/scratch/stefan/7930160/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F) `REAL300000082239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082239 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 49, 28, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 28] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41]) 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: REAL300000082239 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 201, 201, 36, 201, 201, 201, 28, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082239 none O=C([O-])C1=CC(N=NC2CCCC3=C2SC(C2=CC=CC=C2F)=N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 88, 88, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082239 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082239 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082239/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082239/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082239 Building REAL300000082240 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082240' /scratch/stefan/7930160/working/building/REAL300000082240 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082240 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082240/0 /scratch/stefan/7930160/working/building/REAL300000082240 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/253 `/scratch/stefan/7930160/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=CC=C1F) `REAL300000082240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082240 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [138, 107, 138, 107, 107, 40, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 107, 107, 107, 107, 107, 39, 8, 1, 5, 5, 1, 5, 107, 107] 199 rigid atoms, others: [8, 9, 10, 11, 12, 13, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082240 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 70, 70, 107, 107, 107, 107, 199, 199, 107, 199, 199, 199, 199, 199, 107, 1, 1, 1, 1, 1, 13, 69, 107, 199, 199, 107, 199, 1, 1] 199 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]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082240 none O=C([O-])C1=CC(NN=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.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, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 101, 27, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 199, 199, 199, 199, 199, 101, 27, 5, 1, 1, 1, 1, 199, 199] 199 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082240 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082240 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082240/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082240 Building REAL300000082241 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082241' /scratch/stefan/7930160/working/building/REAL300000082241 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082241 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082241/0 /scratch/stefan/7930160/working/building/REAL300000082241 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/254 `/scratch/stefan/7930160/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1F) `REAL300000082241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082241 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 27, 36, 27, 27, 15, 3, 3, 1, 1, 1, 1, 1, 1, 12, 46, 46, 46, 73, 73, 1, 1, 27, 27, 27, 27, 27, 14, 3, 1, 1, 1, 1, 27, 27] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082241 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 4, 16, 16, 27, 27, 16, 27, 98, 162, 162, 162, 201, 201, 27, 27, 1, 1, 1, 1, 1, 4, 16, 27, 27, 27, 27, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082241 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082241 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082241/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082241 Building REAL300000082242 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082242' /scratch/stefan/7930160/working/building/REAL300000082242 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082242 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082242/0 /scratch/stefan/7930160/working/building/REAL300000082242 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/255 `/scratch/stefan/7930160/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2CCCCC2)C2=NC=CC=N2)=CC=C1F) `REAL300000082242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082242 none O=C([O-])C1=CC(N=NC(CC2CCCCC2)C2=NC=CC=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 160, 192, 160, 160, 62, 62, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 42, 42, 14, 42, 42, 160, 160, 160, 160, 160, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 16, 42, 160, 160] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45]) 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: REAL300000082242 none O=C([O-])C1=CC(N=NC(CC2CCCCC2)C2=NC=CC=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 53, 131, 160, 160, 160, 160, 160, 53, 111, 111, 53, 111, 111, 1, 1, 1, 1, 1, 53, 131, 131, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 111, 70, 111, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082242 none O=C([O-])C1=CC(N=NC(CC2CCCCC2)C2=NC=CC=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 117, 153, 117, 117, 46, 46, 10, 1, 10, 33, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 10, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 117, 117] 201 rigid atoms, others: [8, 41, 42, 43, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45]) total number of confs: 483 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082242 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082242 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082242/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082242 Building REAL300000082243 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082243' /scratch/stefan/7930160/working/building/REAL300000082243 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082243 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082243/0 /scratch/stefan/7930160/working/building/REAL300000082243 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/256 `/scratch/stefan/7930160/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1) `REAL300000082243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082243 none CC(C)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [8, 6, 8, 1, 6, 19, 19, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 6, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [19, 33, 34, 3, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 35, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 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: REAL300000082243 none CC(C)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 36, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 52, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 36, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58] 58 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 363 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082243 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082243 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082243/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082243 Building REAL300000082244 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082244' /scratch/stefan/7930160/working/building/REAL300000082244 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082244 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082244/0 /scratch/stefan/7930160/working/building/REAL300000082244 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/257 `/scratch/stefan/7930160/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F) `REAL300000082244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082244 none CC1=NN(C)C(C)=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 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 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, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 52, 52, 52, 151, 151, 151, 151, 151, 151, 151, 151, 151, 10, 1, 1, 1] 151 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000082244 none CC1=NN(C)C(C)=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 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 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, 7, 7, 41, 151, 151, 151, 151, 151, 151, 151, 151, 151, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 41, 151, 151, 151] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082244 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082244 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082244/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082244 Building REAL300000082245 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082245' /scratch/stefan/7930160/working/building/REAL300000082245 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082245 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082245/0 /scratch/stefan/7930160/working/building/REAL300000082245 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/258 `/scratch/stefan/7930160/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=C(Br)C=CC=C32)=CC=C1F) `REAL300000082245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082245 none O=C([O-])C1=CC(NN=C2CCCOC3=C(Br)C=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 33, 33, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082245 none O=C([O-])C1=CC(NN=C2CCCOC3=C(Br)C=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 33, 1, 1, 1, 1, 1, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082245 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082245 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082245/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082245 Building REAL300000082246 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082246' /scratch/stefan/7930160/working/building/REAL300000082246 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082246 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082246/0 /scratch/stefan/7930160/working/building/REAL300000082246 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/259 `/scratch/stefan/7930160/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=C(Cl)C=CC=C32)=CC=C1F) `REAL300000082246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082246 none O=C([O-])C1=CC(NN=C2CCCOC3=C(Cl)C=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 33, 33, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082246 none O=C([O-])C1=CC(NN=C2CCCOC3=C(Cl)C=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 33, 1, 1, 1, 1, 1, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082246 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082246 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082246/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082246 Building REAL300000082247 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082247' /scratch/stefan/7930160/working/building/REAL300000082247 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082247 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082247/0 /scratch/stefan/7930160/working/building/REAL300000082247 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/260 `/scratch/stefan/7930160/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(OCCCC3=CC=CC=C3)=C2)=CC=C1F) `REAL300000082247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082247 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCCCC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 40, 29, 29, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 13, 33, 52, 52, 52, 52, 52, 52, 1, 29, 29, 28, 28, 29, 16, 6, 1, 1, 1, 13, 13, 33, 33, 52, 52, 52, 52, 52, 52, 52, 1, 29, 29] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 338 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082247 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCCCC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 29, 29, 29, 29, 29, 78, 109, 183, 201, 201, 201, 201, 201, 201, 29, 1, 1, 1, 1, 1, 5, 13, 29, 29, 29, 109, 109, 183, 183, 201, 201, 201, 201, 201, 201, 201, 29, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 781 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082247 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCCCC3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 172, 132, 132, 52, 52, 51, 52, 52, 21, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 172, 132, 51, 52, 52, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48]) total number of confs: 519 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082247 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082247 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082247/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082247 Building REAL300000082248 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082248' /scratch/stefan/7930160/working/building/REAL300000082248 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082248 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082248/0 /scratch/stefan/7930160/working/building/REAL300000082248 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/261 `/scratch/stefan/7930160/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=CC=C1F)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082248 none CC(CCC1=CC=CC=C1F)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 9, 46, 98, 116, 201, 201, 163, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 46, 46, 106, 106, 110, 116, 201, 201, 201, 201, 1, 1, 1] 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]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082248 none CC(CCC1=CC=CC=C1F)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 7, 7, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082248 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082248 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082248/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082248 Building REAL300000082249 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082249' /scratch/stefan/7930160/working/building/REAL300000082249 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082249 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082249/0 /scratch/stefan/7930160/working/building/REAL300000082249 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/262 `/scratch/stefan/7930160/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(C#N)C=C2)N=C1) `REAL300000082249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082249 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(C#N)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 49, 135, 135, 135, 135, 135, 135, 177, 177, 135, 1, 1, 1, 1, 1, 3, 3, 1, 1, 2, 3, 3, 1, 1, 10, 10, 10, 48, 135, 135, 135, 2, 2, 2, 3, 3, 3, 3, 1] 177 rigid atoms, others: [1, 42, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 426 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082249 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(C#N)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 135, 135, 135, 135, 177, 177, 124, 135, 177, 177, 177, 135, 135, 46, 46, 46, 10, 1, 1, 1, 135, 135, 135, 177, 177, 177, 177, 135] 177 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 522 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082249 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=C(C#N)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [18, 3, 18, 18, 83, 177, 177, 177, 177, 177, 177, 177, 177, 177, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 18, 18, 83, 177, 177, 177, 3, 3, 3, 1, 1, 1, 1, 3] 177 rigid atoms, others: [38, 39, 40, 41, 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, 42]) total number of confs: 341 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082249 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082249 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082249/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082249 Building REAL300000082250 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082250' /scratch/stefan/7930160/working/building/REAL300000082250 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082250 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082250/0 /scratch/stefan/7930160/working/building/REAL300000082250 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/263 `/scratch/stefan/7930160/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(N3CCOCC3)N=C3C=CC=CN32)=CC=C1F) `REAL300000082250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082250 none O=C([O-])C1=CC(NN=CC2=C(N3CCOCC3)N=C3C=CC=CN32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [84, 75, 84, 75, 75, 24, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 24, 4, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 75, 75] 88 rigid atoms, others: [41, 40, 39, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 162 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: REAL300000082250 none O=C([O-])C1=CC(NN=CC2=C(N3CCOCC3)N=C3C=CC=CN32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 75, 75, 88, 88, 88, 88, 88, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 11, 41, 88, 88, 88, 88, 88, 88, 88, 88, 75, 75, 75, 75, 1, 1] 88 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082250 none O=C([O-])C1=CC(NN=CC2=C(N3CCOCC3)N=C3C=CC=CN32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 88, 88, 88, 88, 88, 51, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 88, 88] 88 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082250 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082250 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082250/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082250 Building REAL300000082251 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082251' /scratch/stefan/7930160/working/building/REAL300000082251 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082251 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082251/0 /scratch/stefan/7930160/working/building/REAL300000082251 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/264 `/scratch/stefan/7930160/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(F)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082251 none COC1=CC=CC(F)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 172, 172, 172, 74, 172, 172, 172, 51, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 172, 172, 172, 52, 52, 52, 10, 1, 1, 1] 201 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: 630 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082251 none COC1=CC=CC(F)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 1, 1, 13, 13, 13, 62, 172, 172, 172, 172, 172, 172, 199, 199, 172, 4, 4, 4, 1, 1, 1, 13, 13, 13, 62, 172, 172, 172] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 416 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082251 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082251 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082251/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082251 Building REAL300000082252 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082252' /scratch/stefan/7930160/working/building/REAL300000082252 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082252 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082252/0 /scratch/stefan/7930160/working/building/REAL300000082252 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/265 `/scratch/stefan/7930160/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=N2)=CC=C1F) `REAL300000082252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082252 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 50, 51, 50, 50, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 24, 4, 1, 1, 1, 50, 50] 51 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082252 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 12, 41, 41, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 12, 41, 50, 50, 50, 1, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082252 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082252 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082252/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082252 Building REAL300000082253 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082253' /scratch/stefan/7930160/working/building/REAL300000082253 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082253 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082253/0 /scratch/stefan/7930160/working/building/REAL300000082253 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/266 `/scratch/stefan/7930160/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC(F)=CC=C32)=CC=C1F) `REAL300000082253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082253 none O=C([O-])C1=CC(NN=C2CCC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 38 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: REAL300000082253 none O=C([O-])C1=CC(NN=C2CCC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082253 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082253 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082253/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082253 Building REAL300000082254 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082254' /scratch/stefan/7930160/working/building/REAL300000082254 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082254 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082254/0 /scratch/stefan/7930160/working/building/REAL300000082254 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/267 `/scratch/stefan/7930160/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082254 none CCN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 6, 6, 25, 56, 56, 55, 55, 56, 56, 91, 91, 56, 1, 1, 17, 17, 17, 17, 17, 13, 13, 9, 13, 13, 1, 1, 6, 25, 56, 56, 56, 1, 1] 201 rigid atoms, others: [2, 38, 39, 9, 10, 11, 12, 13, 46, 45, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 341 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: REAL300000082254 none CCN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 41, 41, 92, 148, 148, 148, 148, 148, 148, 185, 185, 148, 13, 13, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 13, 13, 41, 92, 148, 148, 148, 13, 13] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 548 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082254 none CCN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 56, 136, 148, 148, 136, 148, 148, 56, 56, 56, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 201, 201, 201, 201, 201, 148, 148, 139, 148, 148, 56, 56, 21, 7, 1, 1, 1, 56, 56] 201 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46]) total number of confs: 792 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082254 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082254 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082254/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082254 Building REAL300000082255 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082255' /scratch/stefan/7930160/working/building/REAL300000082255 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082255 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082255/0 /scratch/stefan/7930160/working/building/REAL300000082255 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/268 `/scratch/stefan/7930160/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C(C)N=C1C) `REAL300000082255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082255 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [9, 1, 9, 9, 53, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 117, 117, 117, 1, 2, 2, 2, 2, 2, 2] 117 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) 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: REAL300000082255 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [49, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 117, 117, 83, 93, 117, 117, 117, 50, 50, 50, 11, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082255 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082255 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082255/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082255 Building REAL300000082256 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082256' /scratch/stefan/7930160/working/building/REAL300000082256 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082256 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082256/0 /scratch/stefan/7930160/working/building/REAL300000082256 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/269 `/scratch/stefan/7930160/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082256 none CS(=O)(=O)C1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 46, 61, 61, 46, 46, 46, 46, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 61, 61, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1] 61 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082256 none CS(=O)(=O)C1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 46, 46, 46, 46, 46, 46, 56, 56, 46, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46] 61 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082256 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082256 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082256/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082256 Building REAL300000082257 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082257' /scratch/stefan/7930160/working/building/REAL300000082257 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082257 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082257/0 /scratch/stefan/7930160/working/building/REAL300000082257 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/270 `/scratch/stefan/7930160/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1) `REAL300000082257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082257 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 49, 114, 114, 114, 114, 114, 114, 120, 120, 114, 1, 4, 4, 4, 4, 4, 4, 4, 1, 11, 49, 114, 114, 114, 4, 4] 120 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000082257 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 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 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, 4, 4, 4, 4, 28, 28, 75, 120, 120, 120, 120, 120, 120, 120, 120, 120, 4, 1, 1, 2, 2, 2, 1, 1, 4, 28, 75, 120, 120, 120, 1, 1] 120 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 36, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082257 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 119, 120, 120, 114, 114, 114, 114, 58, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 114, 120, 120, 120, 120, 120, 120, 120, 114, 58, 13, 1, 1, 1, 120, 120] 120 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082257 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082257 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082257/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082257 Building REAL300000082258 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082258' /scratch/stefan/7930160/working/building/REAL300000082258 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082258 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082258/0 /scratch/stefan/7930160/working/building/REAL300000082258 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/271 `/scratch/stefan/7930160/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082258 none CCS(=O)(=O)CC(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 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, 163, 80, 163, 163, 49, 8, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 80, 80, 49, 49, 49, 49, 1, 1, 1] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 933 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082258 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082258 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082258/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082258 Building REAL300000082259 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082259' /scratch/stefan/7930160/working/building/REAL300000082259 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082259 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082259/0 /scratch/stefan/7930160/working/building/REAL300000082259 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/272 `/scratch/stefan/7930160/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OC(F)F)=C1) `REAL300000082259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082259 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OC(F)F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [87, 63, 31, 63, 63, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 126, 193, 193, 63, 87, 87, 87, 63, 63, 21, 7, 1, 1, 1, 193, 63] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082259 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OC(F)F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 27, 63, 63, 63, 63, 63, 63, 92, 92, 63, 1, 1, 9, 48, 48, 1, 3, 3, 3, 1, 1, 12, 26, 63, 63, 63, 48, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 24, 36, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082259 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082259 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082259/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082259 Building REAL300000082260 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082260' /scratch/stefan/7930160/working/building/REAL300000082260 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082260 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082260/0 /scratch/stefan/7930160/working/building/REAL300000082260 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/273 `/scratch/stefan/7930160/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1CC1) `REAL300000082260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082260 none CC1=CC=CC=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [137, 137, 137, 137, 137, 137, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 84, 84, 137, 137, 137, 137, 137, 137, 137, 11, 1, 1, 1, 84, 84, 84, 84, 84] 142 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 334 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: REAL300000082260 none CC1=CC=CC=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 137, 137, 137, 137, 137, 137, 138, 138, 137, 10, 22, 22, 2, 2, 2, 1, 1, 1, 1, 52, 137, 137, 137, 22, 22, 22, 22, 22] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29] set([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, 37, 38]) total number of confs: 287 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082260 none CC1=CC=CC=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [22, 22, 22, 22, 22, 22, 7, 1, 7, 7, 29, 84, 84, 84, 84, 84, 84, 104, 104, 84, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 29, 84, 84, 84, 1, 1, 1, 1, 1] 142 rigid atoms, others: [34, 35, 36, 37, 38, 7, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 241 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082260 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082260 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082260/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082260 Building REAL300000082261 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082261' /scratch/stefan/7930160/working/building/REAL300000082261 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082261 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082261/0 /scratch/stefan/7930160/working/building/REAL300000082261 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/274 `/scratch/stefan/7930160/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC=C(OC(F)(F)F)C=C32)=CC=C1F) `REAL300000082261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082261 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(OC(F)(F)F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 38, 70, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26, 1, 1, 38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 38, 38] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082261 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(OC(F)(F)F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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] 0 hydrogens 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, 8, 38, 38, 38, 38, 38, 38, 38, 38, 200, 200, 200, 200, 38, 38, 1, 1, 1, 1, 1, 8, 38, 38, 38, 38, 38, 38, 38, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 25, 22, 23, 24, 36, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082261 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082261 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082261/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082261 Building REAL300000082262 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082262' /scratch/stefan/7930160/working/building/REAL300000082262 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082262 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082262/0 /scratch/stefan/7930160/working/building/REAL300000082262 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/275 `/scratch/stefan/7930160/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=C(F)C(C)=C1) `REAL300000082262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082262 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 89, 89, 89, 1, 2, 2, 2, 2, 2, 2, 1] 89 rigid atoms, others: [1, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) 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: REAL300000082262 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 90, 90, 90, 77, 78, 90, 90, 90, 51, 51, 51, 11, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082262 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082262 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082262/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082262 Building REAL300000082263 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082263' /scratch/stefan/7930160/working/building/REAL300000082263 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082263 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082263/0 /scratch/stefan/7930160/working/building/REAL300000082263 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/276 `/scratch/stefan/7930160/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=CC3=CC=CC=C32)=CC=C1F) `REAL300000082263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082263 none O=C([O-])C1=CC(NN=CC2=NC=CC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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, 70, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 70, 12, 1, 1, 1, 1, 1, 1, 133, 133] 133 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000082263 none O=C([O-])C1=CC(NN=CC2=NC=CC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 13, 58, 58, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 13, 58, 133, 133, 133, 133, 133, 133, 1, 1] 133 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082263 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082263 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082263/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082263 Building REAL300000082264 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082264' /scratch/stefan/7930160/working/building/REAL300000082264 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082264 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082264/0 /scratch/stefan/7930160/working/building/REAL300000082264 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/277 `/scratch/stefan/7930160/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC) `REAL300000082264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082264 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 1, 9, 9, 49, 148, 148, 148, 148, 148, 148, 174, 174, 148, 1, 1, 1, 1, 1, 1, 1, 1, 3, 27, 27, 27, 26, 26, 49, 148, 148, 148, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 2, 35, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 445 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082264 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 148, 148, 148, 44, 148, 148, 148, 184, 104, 104, 104, 103, 103, 10, 1, 1, 1, 148, 148, 148, 184, 184, 184] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 851 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082264 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082264 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082264/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082264 Building REAL300000082265 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082265' /scratch/stefan/7930160/working/building/REAL300000082265 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082265 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082265/0 /scratch/stefan/7930160/working/building/REAL300000082265 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/278 `/scratch/stefan/7930160/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1) `REAL300000082265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082265 none CC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 166, 107, 166, 166, 93, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 66, 66, 166, 166, 166, 166, 166, 166, 166, 93, 93, 37, 1, 1, 1, 66, 66, 66, 66, 66, 166] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 913 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082265 none CC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 11, 71, 71, 166, 166, 166, 166, 166, 166, 193, 193, 166, 11, 27, 27, 1, 2, 2, 2, 1, 1, 1, 2, 2, 11, 166, 166, 166, 27, 27, 27, 27, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082265 none CC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 18, 27, 27, 15, 5, 1, 5, 23, 23, 67, 67, 67, 67, 67, 67, 103, 103, 67, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 15, 15, 5, 67, 67, 67, 1, 1, 1, 1, 1, 27] 201 rigid atoms, others: [36, 37, 38, 7, 40, 39, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082265 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082265 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082265/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082265 Building REAL300000082266 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082266' /scratch/stefan/7930160/working/building/REAL300000082266 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082266 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082266/0 /scratch/stefan/7930160/working/building/REAL300000082266 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/279 `/scratch/stefan/7930160/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F) `REAL300000082266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082266 none CCN(CC)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [192, 142, 75, 142, 188, 75, 75, 75, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 192, 192, 192, 192, 192, 188, 188, 188, 188, 188, 75, 75, 21, 4, 1, 1, 1, 75] 195 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42]) total number of confs: 913 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082266 none CCN(CC)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 6, 14, 1, 1, 1, 1, 1, 8, 8, 43, 75, 75, 74, 74, 75, 75, 112, 112, 75, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 8, 43, 75, 75, 75, 1] 195 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 42, 22, 23, 24] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082266 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082266 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082266/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082266 Building REAL300000082267 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082267' /scratch/stefan/7930160/working/building/REAL300000082267 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082267 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082267/0 /scratch/stefan/7930160/working/building/REAL300000082267 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/280 `/scratch/stefan/7930160/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082267 none CCCC(CCC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 113, 48, 8, 48, 114, 136, 145, 145, 139, 145, 145, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 136, 136, 136, 129, 136, 123, 123, 48, 126, 126, 136, 130, 145, 145, 145, 145, 145, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 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, 38, 39, 40]) total number of confs: 1067 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082267 none CCCC(CCC1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 16, 4, 3, 1, 1, 1, 1, 1, 1, 1, 16, 61, 61, 145, 145, 145, 145, 145, 145, 166, 166, 145, 46, 46, 46, 46, 46, 41, 41, 16, 4, 4, 3, 3, 1, 1, 1, 1, 1, 145, 145, 145] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082267 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082267 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082267/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082267 Building REAL300000082268 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082268' /scratch/stefan/7930160/working/building/REAL300000082268 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082268 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082268/0 /scratch/stefan/7930160/working/building/REAL300000082268 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/281 `/scratch/stefan/7930160/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1) `REAL300000082268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082268 none CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 6, 11, 11, 6, 1, 6, 6, 17, 39, 39, 39, 39, 39, 39, 40, 40, 39, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 17, 39, 39, 39, 1, 1, 1, 1] 40 rigid atoms, others: [5, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 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: REAL300000082268 none CC(C)(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 40, 40, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 39, 39, 25, 31, 39, 39, 40, 40, 40, 40, 40, 40, 40, 40, 40, 34, 34, 8, 1, 1, 1, 39, 39, 39, 39] 40 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17, 39] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082268 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082268 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082268/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082268 Building REAL300000082269 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082269' /scratch/stefan/7930160/working/building/REAL300000082269 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082269 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082269/0 /scratch/stefan/7930160/working/building/REAL300000082269 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/282 `/scratch/stefan/7930160/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1) `REAL300000082269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082269 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 7, 1, 7, 7, 30, 84, 84, 84, 84, 84, 84, 87, 87, 84, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 12, 12, 30, 84, 84, 84, 1, 1, 1, 1] 90 rigid atoms, others: [4, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 192 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: REAL300000082269 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [81, 80, 81, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 84, 84, 48, 67, 84, 84, 81, 81, 81, 81, 81, 81, 81, 80, 80, 11, 1, 1, 1, 84, 84, 84, 84] 90 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 440 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082269 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082269 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082269/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082269 Building REAL300000082270 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082270' /scratch/stefan/7930160/working/building/REAL300000082270 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082270 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082270/0 /scratch/stefan/7930160/working/building/REAL300000082270 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/283 `/scratch/stefan/7930160/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C2C=CSC2=C1) `REAL300000082270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082270 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 59, 152, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 152, 152, 152, 1, 1, 1, 1] 152 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 279 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: REAL300000082270 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 152, 152, 152, 152, 152, 152, 152, 152, 53, 53, 53, 11, 1, 1, 1, 152, 152, 152, 152] 152 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 227 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082270 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082270 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082270/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082270 Building REAL300000082271 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082271' /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000082271 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082271/0 /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/284 `/scratch/stefan/7930160/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[N@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1C[N@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 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: [17, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 61, 61, 80, 80, 80, 80, 80, 80, 80, 80, 80, 17, 17, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 17, 17, 17, 17, 17, 80, 80, 80] 80 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1C[N@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 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, 8, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 23, 23, 34, 34, 23, 2, 2, 2, 1, 1, 1, 8, 8, 17, 17, 17, 17, 1, 1, 1, 1, 1, 23, 23, 23] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 41, 42, 39, 12, 13, 14, 15, 43, 30, 31] set([6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1C[N@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 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: [23, 23, 23, 23, 23, 23, 45, 80, 80, 80, 80, 80, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 23, 23, 23, 45, 45, 80, 80, 80, 80, 23, 23, 23, 23, 23, 1, 1, 1] 80 rigid atoms, others: [44, 45, 46, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 231 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082271/1 /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/285 `/scratch/stefan/7930160/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[N@@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082271.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1C[N@@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 85, 85, 161, 161, 161, 161, 161, 161, 161, 161, 161, 17, 17, 17, 17, 17, 17, 7, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17, 161, 161, 161] 161 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 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: REAL300000082271 none CC1C[N@@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 10, 10, 43, 43, 43, 43, 43, 43, 68, 68, 43, 2, 2, 2, 1, 1, 1, 7, 7, 17, 17, 17, 17, 1, 1, 1, 1, 1, 43, 43, 43] 161 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 41, 42, 39, 12, 13, 14, 15, 43, 30, 31] set([6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1C[N@@H+](CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 72, 161, 161, 161, 161, 161, 43, 43, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 43, 43, 43, 72, 72, 161, 161, 161, 161, 43, 43, 43, 43, 43, 1, 1, 1] 161 rigid atoms, others: [44, 45, 46, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `2' /scratch/stefan/7930160/working/building/REAL300000082271/2 /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 2 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/286 `/scratch/stefan/7930160/working/3D/286' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082271.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000082271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1CN(CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 22, 9, 9, 1, 1, 1, 1, 22, 22, 22, 22, 22, 201, 201, 201] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1CN(CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 22, 22, 22, 22, 22, 1, 1, 1, 1, 10, 10, 42, 42, 42, 42, 42, 42, 68, 68, 42, 2, 2, 2, 1, 1, 1, 9, 9, 22, 22, 22, 22, 1, 1, 1, 1, 1, 42, 42, 42] 201 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 40, 41, 42, 11, 12, 13, 14, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082271 none CC1CN(CC2=CC=CC=N2)CCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 42, 91, 201, 201, 201, 201, 201, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 42, 42, 42, 42, 42, 91, 91, 201, 201, 201, 201, 42, 42, 42, 42, 42, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082271 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082271 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082271/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082271/0.* 2: /scratch/stefan/7930160/working/building/REAL300000082271/2.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082271 Building REAL300000082272 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082272' /scratch/stefan/7930160/working/building/REAL300000082272 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082272 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082272/0 /scratch/stefan/7930160/working/building/REAL300000082272 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/287 `/scratch/stefan/7930160/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=CC=C1F) `REAL300000082272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082272 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 94, 94, 94, 94, 94, 37, 7, 1, 1, 1, 94, 94] 94 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000082272 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 66, 66, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 13, 66, 94, 94, 94, 1, 1] 94 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082272 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082272 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082272/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082272 Building REAL300000082273 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082273' /scratch/stefan/7930160/working/building/REAL300000082273 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082273 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082273/0 /scratch/stefan/7930160/working/building/REAL300000082273 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/288 `/scratch/stefan/7930160/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082273 none CN1N=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [107, 108, 108, 108, 108, 108, 56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 108, 108, 108, 108, 108, 56, 10, 1, 1, 1, 108, 108] 108 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082273 none CN1N=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 54, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 2, 2, 2, 1, 11, 54, 108, 108, 108, 1, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082273 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082273 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082273/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082273 Building REAL300000082274 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082274' /scratch/stefan/7930160/working/building/REAL300000082274 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082274 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082274/0 /scratch/stefan/7930160/working/building/REAL300000082274 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/289 `/scratch/stefan/7930160/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2C=CC=CN21) `REAL300000082274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082274 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 48, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 130, 130, 130, 1, 1, 1, 1] 130 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 236 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082274 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [60, 61, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 130, 130, 130, 130, 130, 130, 130, 130, 130, 61, 61, 61, 13, 1, 1, 1, 130, 130, 130, 130] 130 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/7930160/working/building/REAL300000082274 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082274 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082274/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082274 Building REAL300000082275 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082275' /scratch/stefan/7930160/working/building/REAL300000082275 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082275 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082275/0 /scratch/stefan/7930160/working/building/REAL300000082275 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/290 `/scratch/stefan/7930160/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(F)C=C2)=CC=C1F) `REAL300000082275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082275 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 30, 36, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 30, 30] 36 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38]) total number of confs: 69 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: REAL300000082275 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 36, 36, 30, 30, 36, 36, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082275 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 52 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082275 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082275 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082275/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082275 Building REAL300000082276 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082276' /scratch/stefan/7930160/working/building/REAL300000082276 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082276 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082276/0 /scratch/stefan/7930160/working/building/REAL300000082276 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/291 `/scratch/stefan/7930160/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCC2) `REAL300000082276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082276 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 83, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 46, 46, 86, 86, 86, 86, 86, 46, 46, 46, 46, 1, 1, 1, 46, 46, 46, 46, 46, 46] 86 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082276 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 10, 10, 46, 46, 46, 46, 46, 46, 68, 68, 46, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 46, 46, 46, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [35, 2, 3, 4, 5, 6, 39, 38, 34, 18, 19, 20, 21, 36, 27, 28, 29, 30, 37] set([0, 1, 32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 31]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082276 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082276 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082276/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082276 Building REAL300000082277 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082277' /scratch/stefan/7930160/working/building/REAL300000082277 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082277 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082277/0 /scratch/stefan/7930160/working/building/REAL300000082277 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/292 `/scratch/stefan/7930160/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCCS2(=O)=O)=C1) `REAL300000082277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082277 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCCS2(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', '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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 41, 75, 75, 75, 75, 75, 75, 106, 106, 75, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 11, 11, 11, 41, 75, 75, 75, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [1, 34, 35, 36, 43, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) 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: REAL300000082277 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCCS2(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', '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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 75, 75, 75, 75, 75, 201, 201, 201, 201, 201, 201, 75, 19, 19, 19, 5, 1, 1, 1, 75, 75, 75, 201, 201, 201, 201, 201, 201, 75] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082277 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2CCCS2(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', '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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 77, 77, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 77, 77, 77, 163, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 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, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43]) total number of confs: 499 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082277 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082277 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082277/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082277 Building REAL300000082278 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082278' /scratch/stefan/7930160/working/building/REAL300000082278 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082278 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082278/0 /scratch/stefan/7930160/working/building/REAL300000082278 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/293 `/scratch/stefan/7930160/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1N1CCOCC1) `REAL300000082278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082278 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 43, 106, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 43, 106, 106, 106, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 106 rigid atoms, others: [1, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 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: REAL300000082278 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 36, 36, 36, 8, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106] 106 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082278 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 4, 15, 15, 55, 106, 106, 106, 106, 106, 106, 106, 106, 106, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 55, 106, 106, 106, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 106 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 205 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082278 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082278 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082278/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082278 Building REAL300000082279 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082279' /scratch/stefan/7930160/working/building/REAL300000082279 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082279 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082279/0 /scratch/stefan/7930160/working/building/REAL300000082279 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/294 `/scratch/stefan/7930160/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(CCCCC)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082279 none CCCCCC(CCCCC)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 102, 83, 72, 33, 6, 33, 71, 82, 101, 116, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 117, 117, 117, 116, 117, 109, 109, 79, 83, 77, 77, 33, 76, 76, 82, 78, 108, 108, 117, 116, 117, 117, 117, 1, 1, 1] 201 rigid atoms, others: [48, 12, 13, 14, 15, 16, 17, 18, 19, 46, 22, 47] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 996 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082279 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082279 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082279/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082279 Building REAL300000082280 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082280' /scratch/stefan/7930160/working/building/REAL300000082280 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082280 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082280/0 /scratch/stefan/7930160/working/building/REAL300000082280 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/295 `/scratch/stefan/7930160/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F) `REAL300000082280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082280 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [32, 12, 1, 12, 12, 75, 159, 159, 159, 159, 159, 159, 175, 175, 159, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 75, 159, 159, 159, 1, 1, 1] 190 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 470 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082280 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [93, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 159, 159, 159, 159, 159, 159, 159, 93, 93, 93, 93, 93, 8, 1, 1, 1, 159, 159, 159] 190 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 467 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082280 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082280 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082280/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082280 Building REAL300000082281 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082281' /scratch/stefan/7930160/working/building/REAL300000082281 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082281 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082281/0 /scratch/stefan/7930160/working/building/REAL300000082281 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/296 `/scratch/stefan/7930160/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082281 none CC1=CC=CC=C1C1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 13, 13, 49, 49, 49, 49, 49, 49, 72, 72, 49, 1, 7, 7, 7, 7, 6, 7, 7, 1, 1, 1, 1, 49, 49, 49, 1, 1] 123 rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 22, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082281 none CC1=CC=CC=C1C1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 60, 60, 123, 123, 123, 123, 123, 123, 123, 123, 123, 7, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 123, 123, 123, 7, 7] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29] set([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, 37, 38]) total number of confs: 185 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082281 none CC1=CC=CC=C1C1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 123, 49, 49, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 123, 123, 123, 123, 123, 123, 123, 49, 49, 49, 49, 1, 1, 1, 49, 49] 123 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 217 number of broken/clashed sets: 52 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082281 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082281 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082281/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082281 Building REAL300000082282 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082282' /scratch/stefan/7930160/working/building/REAL300000082282 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082282 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082282/0 /scratch/stefan/7930160/working/building/REAL300000082282 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/297 `/scratch/stefan/7930160/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC(C3=CC=CC=C3F)C2)=CC=C1F) `REAL300000082282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082282 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC=C3F)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 60, 89, 60, 60, 13, 13, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 60, 60, 60, 60, 60, 1, 1, 1, 1, 10, 10, 4, 10, 1, 1, 60, 60] 178 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 28, 29, 30, 31, 34, 35]) total number of confs: 214 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082282 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC=C3F)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 9, 9, 60, 60, 60, 178, 178, 60, 178, 178, 178, 60, 1, 1, 1, 1, 1, 60, 60, 60, 60, 178, 178, 138, 178, 60, 60, 1, 1] 178 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 580 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082282 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC=C3F)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 92, 92, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 178, 178, 178, 178, 178, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 178, 178] 178 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 258 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082282 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082282 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082282/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082282 Building REAL300000082283 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082283' /scratch/stefan/7930160/working/building/REAL300000082283 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082283 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082283/0 /scratch/stefan/7930160/working/building/REAL300000082283 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/298 `/scratch/stefan/7930160/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCC2) `REAL300000082283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082283 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 52, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 29, 29, 65, 65, 65, 65, 65, 29, 29, 29, 29, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 65 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 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: REAL300000082283 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [5, 4, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 29, 52, 52, 29, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 34, 32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 140 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082283 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082283 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082283/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082283 Building REAL300000082284 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082284' /scratch/stefan/7930160/working/building/REAL300000082284 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082284 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082284/0 /scratch/stefan/7930160/working/building/REAL300000082284 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/299 `/scratch/stefan/7930160/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082284 none CC(C)C(CC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [108, 46, 108, 9, 46, 87, 98, 98, 87, 98, 98, 98, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 111, 111, 111, 111, 111, 111, 111, 46, 87, 87, 98, 98, 98, 98, 1, 1, 1] 141 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]) total number of confs: 739 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: REAL300000082284 none CC(C)C(CC1=CC=C(F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [22, 9, 22, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 98, 98, 98, 98, 98, 98, 123, 123, 98, 22, 22, 22, 22, 22, 22, 22, 9, 3, 3, 1, 1, 1, 1, 98, 98, 98] 141 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 305 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082284 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082284 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082284/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082284 Building REAL300000082285 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082285' /scratch/stefan/7930160/working/building/REAL300000082285 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082285 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082285/0 /scratch/stefan/7930160/working/building/REAL300000082285 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/300 `/scratch/stefan/7930160/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CCCOC21) `REAL300000082285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082285 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CCCOC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 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: 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: REAL300000082285 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CCCOC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 39, 34, 16, 17, 18, 19, 20, 21, 36, 38, 28, 37] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082285 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082285 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082285/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082285 Building REAL300000082286 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082286' /scratch/stefan/7930160/working/building/REAL300000082286 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082286 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082286/0 /scratch/stefan/7930160/working/building/REAL300000082286 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/301 `/scratch/stefan/7930160/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2O1) `REAL300000082286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082286 none CC1(C)CC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 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, 7, 4, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 73, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 73, 73, 74, 74, 74, 74, 74, 74, 73, 73, 73, 73, 73, 51, 10, 1, 1, 1] 74 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082286 none CC1(C)CC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 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, 7, 4, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 73, 73, 73, 73, 73, 73, 74, 74, 73, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 9, 35, 73, 73, 73] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 34, 22, 23, 33, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082286 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082286 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082286/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082286 Building REAL300000082287 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082287' /scratch/stefan/7930160/working/building/REAL300000082287 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082287 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082287/0 /scratch/stefan/7930160/working/building/REAL300000082287 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/302 `/scratch/stefan/7930160/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1C) `REAL300000082287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082287 none CC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 10, 1, 1, 1, 40, 40, 40] 40 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 65 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: REAL300000082287 none CC1=CC=C2OCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 2, 2, 2] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 10, 21, 22, 23, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082287 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082287 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082287/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082287 Building REAL300000082288 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082288' /scratch/stefan/7930160/working/building/REAL300000082288 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082288 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082288/0 /scratch/stefan/7930160/working/building/REAL300000082288 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/303 `/scratch/stefan/7930160/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CC(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082288 none CC1=CC=CC=C1CC(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 115, 52, 9, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 115, 115, 52, 52, 52, 52, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082288 none CC1=CC=CC=C1CC(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082288 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082288 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082288/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082288 Building REAL300000082289 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082289' /scratch/stefan/7930160/working/building/REAL300000082289 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082289 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082289/0 /scratch/stefan/7930160/working/building/REAL300000082289 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/304 `/scratch/stefan/7930160/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC[N@@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1) `REAL300000082289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082289 none CCOCCC[N@@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 132, 87, 53, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 201, 201, 201, 201, 201, 132, 132, 87, 87, 53, 53, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [44, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 800 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082289 none CCOCCC[N@@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 1, 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, 7] 0 hydrogens 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, 23, 12, 6, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 45, 45, 31, 1, 1, 1, 26, 26, 26, 26, 26, 12, 12, 6, 6, 4, 4, 1, 1, 1, 1, 1, 31, 31, 31, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 39, 45, 40, 50, 41, 23, 24, 25, 49, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082289 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082289/1 /scratch/stefan/7930160/working/building/REAL300000082289 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/305 `/scratch/stefan/7930160/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC[N@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1) `REAL300000082289.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082289 none CCOCCC[N@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 144, 104, 71, 55, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 26, 26, 148, 148, 148, 148, 148, 104, 104, 71, 71, 55, 55, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 26, 26] 148 rigid atoms, others: [44, 42, 43, 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, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 578 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082289 none CCOCCC[N@H+]1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 1, 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, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 17, 9, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 38, 38, 26, 1, 1, 1, 55, 55, 55, 55, 55, 17, 17, 9, 9, 6, 6, 1, 1, 1, 1, 1, 26, 26, 26, 1, 2, 2, 2, 1, 1] 148 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 39, 45, 40, 50, 41, 23, 24, 25, 49, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 46, 47, 48]) total number of confs: 279 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082289 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082289 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082289/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082289/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082289 Building REAL300000082290 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082290' /scratch/stefan/7930160/working/building/REAL300000082290 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082290 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082290/0 /scratch/stefan/7930160/working/building/REAL300000082290 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/306 `/scratch/stefan/7930160/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082290 none CCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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, 118, 118, 118, 118, 118, 36, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 201, 201, 201, 201, 201, 118, 118, 118, 36, 36, 36, 8, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 598 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082290 none CCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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: [8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 118, 118, 118, 118, 118, 118, 154, 154, 118, 1, 9, 9, 9, 8, 8, 2, 2, 2, 9, 9, 9, 43, 118, 118, 118] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 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, 35, 36]) total number of confs: 387 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082290 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082290 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082290/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082290 Building REAL300000082291 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082291' /scratch/stefan/7930160/working/building/REAL300000082291 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082291 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082291/0 /scratch/stefan/7930160/working/building/REAL300000082291 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/307 `/scratch/stefan/7930160/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CS(=O)(=O)C1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082291 none CC(CS(=O)(=O)C1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 8, 56, 97, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 56, 97, 97, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 834 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082291 none CC(CS(=O)(=O)C1=CC=CC=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 20, 20, 20, 20, 8, 8, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082291 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082291 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082291/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082291 Building REAL300000082292 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082292' /scratch/stefan/7930160/working/building/REAL300000082292 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082292 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082292/0 /scratch/stefan/7930160/working/building/REAL300000082292 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/308 `/scratch/stefan/7930160/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C) `REAL300000082292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082292 none CC(C)COC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 201, 122, 54, 54, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 54, 201, 201, 201, 201, 201, 201, 201, 182, 182, 54, 54, 54, 54, 1, 1, 1, 54, 54, 54, 54, 54, 54] 201 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082292 none CC(C)COC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 54, 82, 82, 54, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 16, 16, 1, 1, 1, 1, 54, 54, 54, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 20, 21, 22] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082292 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082292 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082292/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082292 Building REAL300000082293 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082293' /scratch/stefan/7930160/working/building/REAL300000082293 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082293 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082293/0 /scratch/stefan/7930160/working/building/REAL300000082293 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/309 `/scratch/stefan/7930160/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)N=C(N3CCCC3)S2)=CC=C1F) `REAL300000082293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082293 none O=C([O-])C1=CC(NN=CC2=C(Cl)N=C(N3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [106, 82, 106, 82, 82, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 82, 82, 82, 82, 82, 49, 9, 9, 9, 10, 9, 10, 9, 9, 9, 82, 82] 148 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082293 none O=C([O-])C1=CC(NN=CC2=C(Cl)N=C(N3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 30, 30, 80, 80, 80, 80, 80, 148, 148, 148, 148, 80, 1, 1, 1, 1, 1, 6, 30, 148, 148, 148, 148, 148, 148, 148, 148, 1, 1] 148 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082293 none O=C([O-])C1=CC(NN=CC2=C(Cl)N=C(N3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 120, 42, 42, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 149, 149, 149, 149, 149, 120, 43, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149] 149 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082293 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082293 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082293/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082293 Building REAL300000082294 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082294' /scratch/stefan/7930160/working/building/REAL300000082294 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082294 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082294/0 /scratch/stefan/7930160/working/building/REAL300000082294 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/310 `/scratch/stefan/7930160/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(Cl)C=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082294 none CCOC1=CC=C(Cl)C=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 172, 129, 129, 129, 129, 129, 129, 129, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 129, 129, 129, 32, 32, 32, 8, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 433 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082294 none CCOC1=CC=C(Cl)C=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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: [29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 54, 129, 129, 129, 129, 129, 129, 168, 168, 129, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 54, 129, 129, 129] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 490 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082294 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082294 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082294/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082294 Building REAL300000082295 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082295' /scratch/stefan/7930160/working/building/REAL300000082295 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082295 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082295/0 /scratch/stefan/7930160/working/building/REAL300000082295 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/311 `/scratch/stefan/7930160/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C3C=CC(Br)=CN23)=CC=C1F) `REAL300000082295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082295 none O=C([O-])C1=CC(NN=CC2=CN=C3C=CC(Br)=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 163, 80, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 80, 13, 1, 1, 1, 1, 163, 163] 163 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082295 none O=C([O-])C1=CC(NN=CC2=CN=C3C=CC(Br)=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 60, 60, 163, 163, 163, 163, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 12, 60, 163, 163, 163, 163, 1, 1] 163 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082295 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082295 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082295/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082295 Building REAL300000082296 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082296' /scratch/stefan/7930160/working/building/REAL300000082296 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082296 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082296/0 /scratch/stefan/7930160/working/building/REAL300000082296 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/312 `/scratch/stefan/7930160/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1C(CC(C)C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082296 none COC1=CC=C(Cl)C=C1C(CC(C)C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [169, 145, 145, 145, 87, 145, 145, 145, 46, 46, 46, 90, 93, 93, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 169, 169, 169, 145, 145, 145, 90, 90, 93, 93, 93, 93, 93, 93, 93, 10, 1, 1, 1] 176 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 706 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082296 none COC1=CC=C(Cl)C=C1C(CC(C)C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 20, 21, 22, 11, 11, 51, 145, 145, 145, 145, 145, 145, 173, 173, 145, 4, 4, 4, 1, 1, 1, 20, 20, 22, 22, 22, 22, 22, 22, 22, 51, 145, 145, 145] 176 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 437 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082296 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082296 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082296/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082296 Building REAL300000082297 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082297' /scratch/stefan/7930160/working/building/REAL300000082297 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082297 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082297/0 /scratch/stefan/7930160/working/building/REAL300000082297 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/313 `/scratch/stefan/7930160/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CC2CC2)C2=CC=CC=C2)=CC=C1F) `REAL300000082297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082297 none O=C([O-])C1=CC(NN=C(CC2CC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 149, 193, 149, 149, 53, 16, 16, 3, 1, 1, 1, 1, 16, 36, 36, 16, 36, 36, 149, 149, 149, 149, 149, 53, 3, 3, 1, 1, 1, 1, 1, 36, 36, 16, 36, 36, 149, 149] 201 rigid atoms, others: [9, 10, 11, 12, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 513 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082297 none O=C([O-])C1=CC(NN=C(CC2CC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 43, 43, 122, 149, 149, 43, 143, 143, 43, 143, 143, 1, 1, 1, 1, 1, 11, 122, 122, 149, 149, 149, 149, 149, 143, 143, 43, 143, 143, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 806 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082297 none O=C([O-])C1=CC(NN=C(CC2CC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 143, 177, 143, 143, 40, 7, 7, 1, 7, 25, 36, 36, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 40, 25, 25, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 143, 143] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 480 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082297 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082297 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082297/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082297 Building REAL300000082298 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082298' /scratch/stefan/7930160/working/building/REAL300000082298 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082298 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082298/0 /scratch/stefan/7930160/working/building/REAL300000082298 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/314 `/scratch/stefan/7930160/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1) `REAL300000082298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082298 none CC1=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 17, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 58, 128, 128, 128, 128, 128, 128, 156, 156, 128, 47, 47, 47, 47, 47, 47, 3, 3, 1, 1, 1, 1, 1, 58, 128, 128, 128, 47, 47] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082298 none CC1=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 39, 47, 47, 43, 47, 47, 7, 7, 21, 57, 57, 57, 57, 57, 57, 79, 79, 57, 1, 1, 1, 2, 2, 2, 39, 39, 47, 47, 47, 47, 47, 21, 57, 57, 57, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 40, 41, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082298 none CC1=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 24, 24, 24, 112, 128, 128, 120, 128, 128, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 57, 57, 57, 57, 57, 112, 112, 128, 128, 128, 128, 128, 7, 1, 1, 1, 57, 57] 201 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40, 41]) total number of confs: 480 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082298 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082298 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082298/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082298 Building REAL300000082299 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082299' /scratch/stefan/7930160/working/building/REAL300000082299 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082299 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082299/0 /scratch/stefan/7930160/working/building/REAL300000082299 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/315 `/scratch/stefan/7930160/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(SC)C=C1OC) `REAL300000082299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082299 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 63, 63, 63, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 121, 63, 63, 27, 116, 125, 125, 125, 63, 22, 6, 1, 1, 1, 121, 121, 121, 63, 116, 116, 116] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082299 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 8, 8, 30, 63, 63, 63, 63, 63, 63, 89, 89, 63, 1, 1, 9, 1, 1, 1, 3, 4, 4, 4, 1, 8, 30, 63, 63, 63, 9, 9, 9, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 21, 22, 23, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082299 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082299 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082299/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082299 Building REAL300000082300 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082300' /scratch/stefan/7930160/working/building/REAL300000082300 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082300 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082300/0 /scratch/stefan/7930160/working/building/REAL300000082300 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/316 `/scratch/stefan/7930160/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=CC=CC=C2N=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082300 none CCN1C2=CC=CC=C2N=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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, 113, 113, 113, 113, 113, 113, 113, 113, 113, 52, 9, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 155, 155, 155, 155, 155, 113, 113, 113, 113, 52, 52, 52, 52, 1, 1, 1] 155 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 515 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082300 none CCN1C2=CC=CC=C2N=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 113, 113, 113, 113, 113, 113, 116, 116, 113, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 113, 113, 113] 155 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082300 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082300/1 /scratch/stefan/7930160/working/building/REAL300000082300 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/317 `/scratch/stefan/7930160/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=CC=CC=C2N=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082300.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082300 none CCN1C2=CC=CC=C2N=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 109, 109, 109, 109, 109, 109, 109, 109, 109, 59, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 150, 150, 150, 150, 150, 109, 109, 109, 109, 59, 59, 59, 13, 1, 1, 1] 150 rigid atoms, others: [38, 39, 40, 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]) total number of confs: 425 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082300 none CCN1C2=CC=CC=C2N=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 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, 1, 1, 1, 1, 1, 5, 5, 5, 29, 109, 109, 109, 109, 109, 109, 119, 119, 109, 3, 3, 3, 2, 2, 1, 1, 1, 1, 6, 6, 6, 29, 109, 109, 109] 150 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 225 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082300 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082300 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082300/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082300/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082300 Building REAL300000082301 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082301' /scratch/stefan/7930160/working/building/REAL300000082301 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082301 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082301/0 /scratch/stefan/7930160/working/building/REAL300000082301 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/318 `/scratch/stefan/7930160/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082301 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 58, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 58, 58, 58, 28, 6, 1, 1, 1] 58 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082301 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 2, 2, 1, 1, 1, 1, 1, 9, 9, 41, 58, 58, 58, 58, 58, 58, 58, 58, 58, 2, 2, 2, 1, 9, 41, 58, 58, 58] 58 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082301 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082301 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082301/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082301 Building REAL300000082302 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082302' /scratch/stefan/7930160/working/building/REAL300000082302 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082302 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082302/0 /scratch/stefan/7930160/working/building/REAL300000082302 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/319 `/scratch/stefan/7930160/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1CCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082302 none CS(=O)(=O)C1CCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 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, 28, 59, 59, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 59, 59, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1] 59 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082302 none CS(=O)(=O)C1CCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 28, 39, 39, 28, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28] 59 rigid atoms, others: [32, 1, 34, 33, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30, 31] set([0, 35, 2, 3, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082302 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082302 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082302/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082302 Building REAL300000082303 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082303' /scratch/stefan/7930160/working/building/REAL300000082303 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082303 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082303/0 /scratch/stefan/7930160/working/building/REAL300000082303 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/320 `/scratch/stefan/7930160/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC3=CC=CC=C3C=C2)=CC=C1F) `REAL300000082303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082303 none O=C([O-])C1=CC(NN=CC2=NC3=CC=CC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 57, 57, 58, 24, 6, 1, 1, 1, 1, 1, 1, 58, 58] 58 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000082303 none O=C([O-])C1=CC(NN=CC2=NC3=CC=CC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 11, 41, 58, 58, 58, 58, 58, 58, 1, 1] 58 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082303 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082303 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082303/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082303 Building REAL300000082304 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082304' /scratch/stefan/7930160/working/building/REAL300000082304 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082304 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082304/0 /scratch/stefan/7930160/working/building/REAL300000082304 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/321 `/scratch/stefan/7930160/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1) `REAL300000082304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082304 none C=CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 7, 1, 7, 7, 41, 124, 124, 124, 124, 124, 124, 155, 155, 124, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 29, 29, 41, 124, 124, 124, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 35, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 515 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: REAL300000082304 none C=CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 103, 35, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 124, 124, 36, 36, 124, 124, 174, 174, 174, 103, 103, 9, 1, 1, 1, 124, 124, 124, 124] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 832 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082304 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082304 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082304/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082304 Building REAL300000082305 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082305' /scratch/stefan/7930160/working/building/REAL300000082305 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082305 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082305/0 /scratch/stefan/7930160/working/building/REAL300000082305 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/322 `/scratch/stefan/7930160/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2Cl)C2=CC=CC=C2)=CC=C1F) `REAL300000082305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082305 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2Cl)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 106, 35, 35, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 68, 68, 54, 68, 68, 193, 193, 193, 193, 193, 106, 9, 9, 6, 6, 1, 1, 1, 1, 68, 68, 54, 68, 68, 193, 193] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082305 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2Cl)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 24, 127, 149, 193, 193, 149, 193, 193, 193, 24, 46, 46, 37, 46, 46, 1, 1, 1, 1, 1, 7, 127, 127, 149, 149, 193, 193, 190, 193, 46, 46, 37, 46, 46, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 900 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082305 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2Cl)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 71, 46, 46, 19, 4, 4, 1, 4, 31, 38, 68, 68, 38, 68, 68, 68, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 19, 31, 31, 38, 38, 68, 68, 66, 68, 1, 1, 1, 1, 1, 46, 46] 201 rigid atoms, others: [38, 39, 8, 41, 42, 40, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082305 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082305 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082305/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082305 Building REAL300000082306 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082306' /scratch/stefan/7930160/working/building/REAL300000082306 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082306 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082306/0 /scratch/stefan/7930160/working/building/REAL300000082306 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/323 `/scratch/stefan/7930160/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2)=CC=C1F) `REAL300000082306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082306 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 35, 45, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 35, 35] 63 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082306 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 35, 35, 35, 35, 35, 60, 63, 63, 60, 63, 63, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 60, 60, 63, 63, 60, 63, 63, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082306 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 26, 26, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 63, 63] 63 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082306 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082306 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082306/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082306 Building REAL300000082307 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082307' /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000082307 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082307/0 /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/324 `/scratch/stefan/7930160/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(CC2=CC=CC=C2)CCO1) `REAL300000082307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 38, 38, 85, 85, 85, 85, 85, 85, 128, 128, 85, 1, 1, 1, 1, 6, 9, 9, 8, 9, 9, 1, 1, 1, 8, 8, 8, 8, 85, 85, 85, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 44, 45, 14, 15, 16, 17, 46, 24, 25, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 85, 85, 85, 146, 201, 201, 180, 201, 201, 85, 85, 85, 33, 33, 33, 33, 1, 1, 1, 85, 85, 85, 146, 146, 201, 201, 201, 201, 201, 85, 85, 85, 85] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 35, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 35, 35, 35, 201, 201, 201, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 9] 201 rigid atoms, others: [39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47]) total number of confs: 364 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082307/1 /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/325 `/scratch/stefan/7930160/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@H+](CC2=CC=CC=C2)CCO1) `REAL300000082307.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 34, 34, 65, 65, 65, 65, 65, 65, 90, 90, 65, 1, 1, 1, 1, 1, 8, 12, 12, 10, 12, 12, 1, 1, 1, 6, 6, 6, 5, 65, 65, 65, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 1, 1, 1, 1] 126 rigid atoms, others: [1, 35, 36, 37, 48, 47, 45, 14, 15, 16, 17, 18, 46, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 248 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: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 65, 65, 65, 65, 120, 126, 126, 122, 126, 126, 65, 65, 65, 32, 32, 32, 32, 1, 1, 1, 65, 65, 65, 120, 120, 126, 126, 126, 126, 126, 65, 65, 65, 65] 126 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 507 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [31, 12, 31, 92, 92, 126, 126, 126, 126, 126, 126, 126, 126, 126, 12, 11, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 31, 31, 126, 126, 126, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12] 126 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 261 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `2' /scratch/stefan/7930160/working/building/REAL300000082307/2 /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 2 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/326 `/scratch/stefan/7930160/working/3D/326' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@@H+](CC2=CC=CC=C2)CCO1) `REAL300000082307.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000082307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082307/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 34, 34, 65, 65, 65, 65, 65, 65, 91, 91, 65, 1, 1, 1, 1, 1, 8, 12, 12, 8, 12, 12, 1, 1, 1, 6, 6, 6, 6, 65, 65, 65, 1, 1, 1, 8, 8, 12, 12, 8, 12, 12, 1, 1, 1, 1] 128 rigid atoms, others: [1, 35, 36, 37, 48, 47, 45, 14, 15, 16, 17, 18, 46, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 65, 65, 65, 65, 122, 128, 128, 122, 128, 128, 65, 65, 65, 32, 32, 32, 32, 1, 1, 1, 65, 65, 65, 122, 122, 128, 128, 122, 128, 128, 65, 65, 65, 65] 128 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082307 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1C[N@@H+](CC2=CC=CC=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [31, 12, 31, 93, 93, 128, 128, 128, 128, 128, 128, 128, 128, 128, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 31, 31, 128, 128, 128, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12] 128 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 259 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082307 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082307 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082307/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082307/0.* 2: /scratch/stefan/7930160/working/building/REAL300000082307/2.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082307 Building REAL300000082308 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082308' /scratch/stefan/7930160/working/building/REAL300000082308 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082308 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082308/0 /scratch/stefan/7930160/working/building/REAL300000082308 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/327 `/scratch/stefan/7930160/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C2NC(=O)C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082308 none CC1=CC(Br)=C2NC(=O)C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 33, 33, 33, 33, 33, 32, 12, 1, 1, 1, 33] 33 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082308 none CC1=CC(Br)=C2NC(=O)C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 32, 32, 32, 33, 33, 32, 1, 1, 2, 2, 2, 1, 1, 7, 32, 32, 32, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 33, 27, 28] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082308 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082308 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082308/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082308 Building REAL300000082309 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082309' /scratch/stefan/7930160/working/building/REAL300000082309 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082309 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082309/0 /scratch/stefan/7930160/working/building/REAL300000082309 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/328 `/scratch/stefan/7930160/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1) `REAL300000082309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082309 none COCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 54, 12, 1, 12, 12, 64, 124, 124, 124, 124, 124, 124, 156, 156, 124, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 89, 89, 89, 54, 54, 64, 124, 124, 124, 1, 1, 1, 1] 201 rigid atoms, others: [19, 3, 36, 37, 38, 16, 17, 18, 35, 20, 21, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 602 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: REAL300000082309 none COCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 89, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 124, 124, 26, 124, 124, 124, 124, 124, 124, 114, 114, 114, 89, 89, 6, 1, 1, 1, 124, 124, 30, 124] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 596 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082309 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082309 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082309/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082309 Building REAL300000082310 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082310' /scratch/stefan/7930160/working/building/REAL300000082310 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082310 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082310/0 /scratch/stefan/7930160/working/building/REAL300000082310 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/329 `/scratch/stefan/7930160/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl) `REAL300000082310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082310 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 141, 101, 141, 141, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 141, 141, 141, 201, 201, 201, 141, 141, 57, 11, 1, 1, 1, 141] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 521 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082310 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 8, 8, 55, 141, 141, 141, 141, 141, 141, 201, 201, 141, 1, 1, 1, 4, 4, 4, 1, 1, 8, 55, 141, 141, 141, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082310 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082310 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082310/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082310 Building REAL300000082311 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082311' /scratch/stefan/7930160/working/building/REAL300000082311 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082311 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082311/0 /scratch/stefan/7930160/working/building/REAL300000082311 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/330 `/scratch/stefan/7930160/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C=C2)=CC=C1F) `REAL300000082311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082311 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 30, 36, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 30, 30] 36 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38]) total number of confs: 70 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: REAL300000082311 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 36, 36, 35, 36, 36, 36, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082311 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 52 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082311 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082311 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082311/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082311 Building REAL300000082312 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082312' /scratch/stefan/7930160/working/building/REAL300000082312 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082312 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082312/0 /scratch/stefan/7930160/working/building/REAL300000082312 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/331 `/scratch/stefan/7930160/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCCC2) `REAL300000082312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082312 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 26, 26, 26, 26, 26, 44, 44, 44, 44, 44, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 44 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 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: REAL300000082312 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [7, 4, 1, 1, 1, 1, 1, 7, 7, 25, 25, 26, 26, 26, 26, 39, 39, 26, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 34, 35, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28]) total number of confs: 109 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082312 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082312 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082312/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082312 Building REAL300000082313 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082313' /scratch/stefan/7930160/working/building/REAL300000082313 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082313 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082313/0 /scratch/stefan/7930160/working/building/REAL300000082313 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/332 `/scratch/stefan/7930160/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000082313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082313 none CC(C)(C)C1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 13, 13, 2, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 35, 74, 74, 74, 74, 74, 74, 117, 117, 74, 1, 8, 8, 13, 13, 16, 13, 16, 13, 13, 13, 16, 9, 9, 1, 1, 7, 35, 74, 74, 74, 9, 9] 201 rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 40, 25] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 43, 44, 45, 46, 47]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082313 none CC(C)(C)C1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 31, 83, 125, 125, 125, 125, 125, 125, 201, 201, 125, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 8, 31, 83, 125, 125, 125, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 38, 46, 47, 8, 26, 27, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082313 none CC(C)(C)C1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 125, 200, 200, 125, 128, 128, 75, 75, 75, 75, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 128, 128, 200, 200, 200, 200, 200, 200, 200, 200, 200, 128, 128, 75, 75, 35, 9, 1, 1, 1, 128, 128] 200 rigid atoms, others: [43, 44, 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, 40, 41, 42, 46, 47]) total number of confs: 671 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082313 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082313 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082313/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082313 Building REAL300000082314 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082314' /scratch/stefan/7930160/working/building/REAL300000082314 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082314 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082314/0 /scratch/stefan/7930160/working/building/REAL300000082314 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/333 `/scratch/stefan/7930160/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC=C32)=CC=C1F) `REAL300000082314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082314 none O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 38 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: REAL300000082314 none O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082314 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082314 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082314/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082314 Building REAL300000082315 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082315' /scratch/stefan/7930160/working/building/REAL300000082315 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082315 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082315/0 /scratch/stefan/7930160/working/building/REAL300000082315 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/334 `/scratch/stefan/7930160/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=NC=C2)C=C1) `REAL300000082315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082315 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 35, 115, 115, 115, 115, 115, 115, 127, 127, 115, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 7, 7, 7, 35, 115, 115, 115, 1, 1, 3, 3, 3, 3, 1, 1] 127 rigid atoms, others: [1, 34, 33, 40, 39, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 242 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: REAL300000082315 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 115, 115, 115, 115, 127, 127, 115, 127, 127, 115, 115, 54, 54, 54, 10, 1, 1, 1, 115, 115, 127, 127, 127, 127, 115, 115] 127 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082315 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=NC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 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: [12, 3, 12, 12, 58, 127, 127, 127, 127, 127, 127, 127, 127, 127, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 58, 127, 127, 127, 3, 3, 1, 1, 1, 1, 3, 3] 127 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 242 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082315 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082315 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082315/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082315 Building REAL300000082316 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082316' /scratch/stefan/7930160/working/building/REAL300000082316 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082316 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082316/0 /scratch/stefan/7930160/working/building/REAL300000082316 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/335 `/scratch/stefan/7930160/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC(F)=CC=C3O2)=CC=C1F) `REAL300000082316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082316 none O=C([O-])C1=CC(NN=CC2=CC3=CC(F)=CC=C3O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 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, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 36, 6, 1, 1, 1, 1, 69, 69] 69 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082316 none O=C([O-])C1=CC(NN=CC2=CC3=CC(F)=CC=C3O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 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, 10, 48, 48, 68, 68, 69, 68, 68, 69, 69, 68, 69, 1, 1, 1, 1, 1, 10, 48, 69, 69, 69, 69, 1, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082316 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082316 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082316/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082316 Building REAL300000082317 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082317' /scratch/stefan/7930160/working/building/REAL300000082317 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082317 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082317/0 /scratch/stefan/7930160/working/building/REAL300000082317 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/336 `/scratch/stefan/7930160/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082317 none COCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 172, 64, 64, 26, 64, 64, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 64, 201, 201, 201, 172, 172, 45, 64, 64, 26, 7, 1, 1, 1, 64] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082317 none COCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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: [26, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 64, 64, 64, 64, 64, 64, 102, 102, 63, 1, 26, 26, 26, 8, 8, 1, 1, 1, 7, 29, 64, 64, 64, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 35, 21, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082317 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082317 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082317/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082317 Building REAL300000082318 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082318' /scratch/stefan/7930160/working/building/REAL300000082318 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082318 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082318/0 /scratch/stefan/7930160/working/building/REAL300000082318 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/337 `/scratch/stefan/7930160/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=CC=C1F) `REAL300000082318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082318 none O=C([O-])C1=CC(N=NC2CCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 26, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 43, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 38, 39, 40, 41, 44, 45]) 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: REAL300000082318 none O=C([O-])C1=CC(N=NC2CCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082318 none O=C([O-])C1=CC(N=NC2CCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 26, 26] 26 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082318 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082318 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082318/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082318 Building REAL300000082319 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082319' /scratch/stefan/7930160/working/building/REAL300000082319 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082319 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082319/0 /scratch/stefan/7930160/working/building/REAL300000082319 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/338 `/scratch/stefan/7930160/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2)=CC=C1F) `REAL300000082319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082319 none O=C([O-])C1=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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, 7] 0 hydrogens need 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, 198, 198, 84, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 47, 47, 27, 37, 47, 47, 198, 198, 198, 198, 198, 84, 8, 8, 1, 1, 1, 1, 47, 47, 47, 47, 198, 198] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082319 none O=C([O-])C1=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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, 7] 0 hydrogens 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, 8, 33, 33, 167, 198, 198, 198, 198, 198, 33, 56, 56, 33, 51, 56, 56, 1, 1, 1, 1, 1, 8, 167, 167, 198, 198, 198, 198, 56, 56, 56, 56, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082319 none O=C([O-])C1=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 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, 7] 0 hydrogens 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, 56, 77, 56, 56, 15, 4, 4, 1, 4, 26, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 15, 26, 26, 47, 47, 47, 47, 1, 1, 1, 1, 56, 56] 201 rigid atoms, others: [35, 36, 37, 38, 8, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 285 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082319 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082319 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082319/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082319 Building REAL300000082320 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082320' /scratch/stefan/7930160/working/building/REAL300000082320 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000082320 as failed and skipping /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `/scratch/stefan/7930160/failed' `/scratch/stefan/7930160/working/building/REAL300000082320' -> `/scratch/stefan/7930160/failed/REAL300000082320' Building REAL300000082321 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082321' /scratch/stefan/7930160/working/building/REAL300000082321 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082321 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082321/0 /scratch/stefan/7930160/working/building/REAL300000082321 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/339 `/scratch/stefan/7930160/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=C(SC=C2)S1) `REAL300000082321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082321 none C[C@H]1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=C(SC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 1, 1, 1, 17, 17] 17 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 38 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: REAL300000082321 none C[C@H]1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=C(SC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 17, 18, 19, 20, 21, 22, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082321 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082321 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082321/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082321 Building REAL300000082322 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082322' /scratch/stefan/7930160/working/building/REAL300000082322 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082322 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082322/0 /scratch/stefan/7930160/working/building/REAL300000082322 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/340 `/scratch/stefan/7930160/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1) `REAL300000082322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082322 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 49, 111, 111, 111, 111, 111, 111, 124, 124, 111, 1, 1, 1, 1, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 10, 10, 10, 48, 111, 111, 110, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [1, 47, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082322 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 110, 111, 110, 110, 201, 201, 201, 193, 201, 201, 201, 110, 110, 34, 34, 34, 8, 1, 1, 1, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 372 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082322 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 24, 24, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 102, 201, 201, 201, 5, 5, 5, 1, 2, 2, 2, 1, 1, 2, 2, 2, 5] 201 rigid atoms, others: [38, 42, 43, 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, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 417 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082322 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082322 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082322/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082322 Building REAL300000082323 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082323' /scratch/stefan/7930160/working/building/REAL300000082323 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082323 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082323/0 /scratch/stefan/7930160/working/building/REAL300000082323 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/341 `/scratch/stefan/7930160/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2OC(F)F)OCO3)=CC=C1F) `REAL300000082323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082323 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2OC(F)F)OCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [97, 59, 97, 59, 59, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 45, 1, 1, 1, 59, 59, 59, 59, 59, 25, 4, 1, 1, 44, 1, 1, 59, 59] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 16, 17, 18, 35, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082323 none O=C([O-])C1=CC(NN=CC2=CC3=C(C=C2OC(F)F)OCO3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 3, 1, 1, 1, 1, 9, 32, 32, 59, 59, 59, 59, 59, 59, 153, 201, 201, 59, 59, 59, 1, 1, 1, 1, 1, 9, 32, 59, 59, 201, 59, 59, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082323 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082323 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082323/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082323 Building REAL300000082324 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082324' /scratch/stefan/7930160/working/building/REAL300000082324 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082324 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082324/0 /scratch/stefan/7930160/working/building/REAL300000082324 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/342 `/scratch/stefan/7930160/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000082324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082324 none CCC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 12, 12, 1, 1, 1, 1, 1, 1, 8, 8, 34, 70, 70, 70, 70, 70, 70, 93, 93, 70, 1, 12, 12, 16, 16, 16, 16, 16, 12, 12, 1, 1, 8, 34, 70, 70, 70, 12, 12] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082324 none CCC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 52, 52, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 4, 4, 4, 4, 4, 1, 1, 12, 12, 52, 154, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082324 none CCC1=CC=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 140, 201, 201, 70, 70, 70, 70, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 29, 7, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40, 41]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082324 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082324 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082324/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082324 Building REAL300000082325 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082325' /scratch/stefan/7930160/working/building/REAL300000082325 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082325 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082325/0 /scratch/stefan/7930160/working/building/REAL300000082325 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/343 `/scratch/stefan/7930160/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082325 none N#CC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1] 36 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 61 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: REAL300000082325 none N#CC1=CC=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32] set([33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 54 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082325 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082325 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082325/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082325 Building REAL300000082326 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082326' /scratch/stefan/7930160/working/building/REAL300000082326 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082326 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082326/0 /scratch/stefan/7930160/working/building/REAL300000082326 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/344 `/scratch/stefan/7930160/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=NC=C3)=C2)=CC=C1F) `REAL300000082326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082326 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=NC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 201, 139, 139, 59, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 139, 139, 138, 138, 139, 59, 11, 1, 1, 1, 3, 3, 3, 3, 1, 139, 139] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36, 37]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082326 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=NC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 10, 54, 54, 139, 139, 139, 139, 139, 201, 201, 201, 201, 201, 139, 1, 1, 1, 1, 1, 10, 54, 139, 139, 139, 201, 201, 201, 201, 139, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082326 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=NC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 99, 20, 20, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 201, 201, 201, 201, 201, 99, 20, 3, 3, 3, 1, 1, 1, 1, 3, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082326 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082326 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082326/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082326 Building REAL300000082327 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082327' /scratch/stefan/7930160/working/building/REAL300000082327 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082327 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082327/0 /scratch/stefan/7930160/working/building/REAL300000082327 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/345 `/scratch/stefan/7930160/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC3=CC=C(Cl)C=C3C2)=CC=C1F) `REAL300000082327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082327 none O=C([O-])C1=CC(N=NC2CC3=CC=C(Cl)C=C3C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 31]) 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: REAL300000082327 none O=C([O-])C1=CC(N=NC2CC3=CC=C(Cl)C=C3C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 8, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082327 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082327 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082327/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082327 Building REAL300000082328 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082328' /scratch/stefan/7930160/working/building/REAL300000082328 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082328 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082328/0 /scratch/stefan/7930160/working/building/REAL300000082328 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/346 `/scratch/stefan/7930160/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(CC2=CC=CC=N2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082328 none CC1=CC=C(C(CC2=CC=CC=N2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 79, 79, 33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 98, 167, 167, 167, 167, 167, 167, 178, 178, 167, 79, 79, 79, 79, 79, 79, 79, 9, 9, 1, 1, 1, 1, 98, 167, 167, 167, 79, 79] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 746 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082328 none CC1=CC=C(C(CC2=CC=CC=N2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 34, 78, 78, 78, 78, 78, 9, 9, 54, 98, 98, 98, 98, 98, 98, 119, 119, 98, 1, 1, 2, 2, 2, 1, 1, 34, 34, 78, 78, 78, 78, 54, 98, 98, 98, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 452 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082328 none CC1=CC=C(C(CC2=CC=CC=N2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 88, 88, 22, 22, 22, 98, 167, 167, 167, 167, 167, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 88, 88, 88, 88, 88, 88, 88, 98, 98, 167, 167, 167, 167, 5, 1, 1, 1, 88, 88] 201 rigid atoms, others: [39, 40, 41, 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, 42, 43]) total number of confs: 870 number of broken/clashed sets: 48 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082328 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082328 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082328/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082328 Building REAL300000082329 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082329' /scratch/stefan/7930160/working/building/REAL300000082329 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082329 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082329/0 /scratch/stefan/7930160/working/building/REAL300000082329 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/347 `/scratch/stefan/7930160/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OC2CCCC2)=CC=C1F) `REAL300000082329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082329 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 101, 66, 66, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 66, 66, 66, 66, 66, 31, 8, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 66, 66] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 309 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: REAL300000082329 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 28, 66, 66, 66, 31, 66, 66, 66, 160, 201, 201, 201, 201, 1, 1, 1, 1, 1, 8, 28, 66, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 539 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082329 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OC2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 152, 49, 49, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 49, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 470 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082329 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082329 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082329/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082329 Building REAL300000082330 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082330' /scratch/stefan/7930160/working/building/REAL300000082330 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082330 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082330/0 /scratch/stefan/7930160/working/building/REAL300000082330 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/348 `/scratch/stefan/7930160/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C) `REAL300000082330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082330 none CC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 58, 58, 58, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 58, 58, 58, 58, 58, 58, 116, 40, 10, 1, 1, 1, 58, 58, 58, 58] 116 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 275 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082330 none CC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 8, 8, 33, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 2, 2, 2, 1, 2, 8, 33, 58, 58, 58, 1, 2, 2, 2] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 19, 20, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082330 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082330 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082330/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082330 Building REAL300000082331 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082331' /scratch/stefan/7930160/working/building/REAL300000082331 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082331 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082331/0 /scratch/stefan/7930160/working/building/REAL300000082331 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/349 `/scratch/stefan/7930160/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CN=CC=N3)C=C2)=CC=C1F) `REAL300000082331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082331 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CN=CC=N3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 35, 55, 35, 35, 14, 4, 4, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 35, 1, 1, 35, 35, 35, 35, 35, 14, 4, 1, 1, 35, 35, 35, 1, 1, 35, 35] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082331 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CN=CC=N3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 25, 35, 35, 25, 27, 127, 201, 201, 201, 201, 201, 35, 35, 1, 1, 1, 1, 1, 7, 25, 35, 35, 201, 201, 201, 35, 35, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 25, 22, 23, 24, 36, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082331 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CN=CC=N3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 137, 61, 61, 35, 13, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 137, 61, 35, 35, 1, 1, 1, 35, 35, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 527 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082331 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082331 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082331/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082331 Building REAL300000082332 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082332' /scratch/stefan/7930160/working/building/REAL300000082332 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082332 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082332/0 /scratch/stefan/7930160/working/building/REAL300000082332 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/350 `/scratch/stefan/7930160/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CCCO2)=CC=C1F) `REAL300000082332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082332 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CCCO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 31, 31, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 80, 80, 80, 80, 31, 31, 31, 31, 31, 18, 5, 1, 1, 1, 31, 31, 80, 80, 80, 80, 80, 80, 80, 31, 31] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082332 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CCCO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 16, 31, 31, 31, 17, 31, 31, 31, 88, 160, 201, 201, 201, 201, 1, 1, 1, 1, 1, 4, 16, 31, 31, 31, 160, 160, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082332 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CCCO2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 176, 121, 121, 80, 80, 80, 80, 80, 80, 80, 30, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 121, 80, 80, 80, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 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, 42, 43]) total number of confs: 502 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082332 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082332 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082332/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082332 Building REAL300000082333 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082333' /scratch/stefan/7930160/working/building/REAL300000082333 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082333 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082333/0 /scratch/stefan/7930160/working/building/REAL300000082333 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/351 `/scratch/stefan/7930160/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C#N) `REAL300000082333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082333 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C#N 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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, 144, 144, 144, 144, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 144, 144, 144, 144, 201, 201, 201, 144, 144, 60, 13, 1, 1, 1, 144] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082333 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C#N 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 57, 144, 144, 143, 143, 144, 144, 201, 201, 144, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 57, 144, 144, 144, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 19, 20, 21, 22, 26, 27] set([0, 32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082333 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082333 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082333/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082333 Building REAL300000082334 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082334' /scratch/stefan/7930160/working/building/REAL300000082334 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082334 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082334/0 /scratch/stefan/7930160/working/building/REAL300000082334 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/352 `/scratch/stefan/7930160/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C(F)=C1) `REAL300000082334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082334 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 11, 54, 131, 131, 131, 1, 1, 5, 5, 5, 1] 201 rigid atoms, others: [32, 1, 37, 33, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082334 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 131, 131, 131, 131, 201, 201, 201, 131, 131, 131, 40, 40, 40, 10, 1, 1, 1, 131, 131, 201, 201, 201, 131] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 617 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082334 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082334 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082334/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082334 Building REAL300000082335 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082335' /scratch/stefan/7930160/working/building/REAL300000082335 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082335 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082335/0 /scratch/stefan/7930160/working/building/REAL300000082335 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/353 `/scratch/stefan/7930160/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F) `REAL300000082335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082335 none CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 124, 124, 26, 26, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 124, 124, 124, 201, 201, 201, 124, 124, 26, 26, 26, 7, 1, 1, 1, 124] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 314 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082335 none CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 124, 124, 124, 124, 124, 124, 155, 155, 124, 1, 1, 1, 10, 10, 10, 1, 1, 13, 13, 13, 57, 124, 124, 124, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 382 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082335 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082335 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082335/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082335 Building REAL300000082336 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082336' /scratch/stefan/7930160/working/building/REAL300000082336 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082336 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082336/0 /scratch/stefan/7930160/working/building/REAL300000082336 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/354 `/scratch/stefan/7930160/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)F)C=C1) `REAL300000082336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082336 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 71, 71, 71, 71, 71, 71, 98, 98, 71, 1, 1, 1, 1, 1, 8, 28, 59, 59, 1, 1, 6, 6, 6, 30, 71, 71, 71, 1, 1, 28, 28, 60, 1, 1] 201 rigid atoms, others: [32, 1, 37, 38, 33, 14, 15, 16, 17, 18, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082336 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 71, 71, 27, 47, 131, 167, 201, 201, 71, 71, 28, 28, 28, 6, 1, 1, 1, 71, 71, 166, 166, 201, 71, 71] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082336 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082336 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082336/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082336 Building REAL300000082337 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082337' /scratch/stefan/7930160/working/building/REAL300000082337 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082337 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082337/0 /scratch/stefan/7930160/working/building/REAL300000082337 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/355 `/scratch/stefan/7930160/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)(F)F)C=C1) `REAL300000082337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082337 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 68, 68, 68, 68, 68, 68, 91, 91, 68, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 1, 1, 6, 6, 6, 30, 68, 68, 68, 1, 1, 32, 32, 1, 1] 201 rigid atoms, others: [1, 34, 37, 38, 33, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 321 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082337 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 68, 68, 29, 67, 160, 201, 201, 201, 201, 68, 68, 26, 26, 26, 5, 1, 1, 1, 68, 68, 201, 201, 68, 68] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 574 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082337 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082337 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082337/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082337 Building REAL300000082338 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082338' /scratch/stefan/7930160/working/building/REAL300000082338 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082338 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082338/0 /scratch/stefan/7930160/working/building/REAL300000082338 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/356 `/scratch/stefan/7930160/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082338 none COCC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 153, 106, 79, 106, 106, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 106, 106, 201, 201, 201, 153, 153, 106, 106, 48, 11, 1, 1, 1, 106, 106] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082338 none COCC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [18, 4, 1, 1, 1, 1, 1, 1, 8, 8, 47, 106, 106, 106, 106, 106, 106, 150, 150, 106, 1, 1, 19, 19, 19, 4, 4, 1, 1, 8, 47, 106, 106, 106, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082338 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082338 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082338/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082338 Building REAL300000082339 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082339' /scratch/stefan/7930160/working/building/REAL300000082339 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082339 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082339/0 /scratch/stefan/7930160/working/building/REAL300000082339 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/357 `/scratch/stefan/7930160/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Br)=CC=C1F) `REAL300000082339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082339 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 50, 10, 1, 1, 1, 78, 78] 78 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082339 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 78, 78, 78, 54, 78, 78, 78, 1, 1, 1, 1, 1, 10, 40, 78, 54, 78, 1, 1] 78 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082339 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082339 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082339/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082339 Building REAL300000082340 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082340' /scratch/stefan/7930160/working/building/REAL300000082340 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082340 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082340/0 /scratch/stefan/7930160/working/building/REAL300000082340 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/358 `/scratch/stefan/7930160/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1) `REAL300000082340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082340 none CC1=C(C)C=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 5, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 64, 64, 64, 64, 64, 64, 63, 42, 10, 1, 1, 1, 63, 63] 64 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) 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: REAL300000082340 none CC1=C(C)C=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 5, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 64, 64, 64, 64, 64, 64, 64, 64, 63, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 6, 36, 64, 64, 63, 1, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 36, 30, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082340 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082340 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082340/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082340 Building REAL300000082341 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082341' /scratch/stefan/7930160/working/building/REAL300000082341 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082341 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082341/0 /scratch/stefan/7930160/working/building/REAL300000082341 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/359 `/scratch/stefan/7930160/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082341 none COCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 196, 164, 69, 69, 69, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 201, 201, 201, 196, 196, 164, 164, 69, 29, 9, 1, 1, 1, 69] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082341 none COCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 13, 9, 1, 1, 1, 1, 1, 7, 7, 36, 69, 69, 69, 69, 69, 69, 94, 94, 69, 1, 1, 35, 35, 35, 13, 13, 9, 9, 1, 7, 36, 69, 69, 69, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 35, 20, 21, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082341 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082341 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082341/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082341 Building REAL300000082342 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082342' /scratch/stefan/7930160/working/building/REAL300000082342 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082342 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082342/0 /scratch/stefan/7930160/working/building/REAL300000082342 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/360 `/scratch/stefan/7930160/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082342 none CCOC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 187, 187, 89, 187, 55, 20, 20, 28, 28, 12, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 201, 201, 201, 201, 201, 86, 86, 28, 27, 11, 4, 1, 1, 1, 28, 28] 201 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082342 none CCOC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 48, 48, 9, 48, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 27, 27, 27, 27, 27, 28, 36, 36, 27, 1, 1, 86, 86, 86, 85, 85, 9, 9, 1, 1, 6, 15, 27, 27, 27, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082342 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082342 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082342/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082342 Building REAL300000082343 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082343' /scratch/stefan/7930160/working/building/REAL300000082343 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082343 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082343/0 /scratch/stefan/7930160/working/building/REAL300000082343 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/361 `/scratch/stefan/7930160/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1) `REAL300000082343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082343 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 28, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 65, 65, 65, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 1, 34, 35, 36, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082343 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [42, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 65, 65, 65, 65, 65, 65, 65, 65, 65, 43, 43, 43, 11, 1, 1, 1, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082343 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082343/1 /scratch/stefan/7930160/working/building/REAL300000082343 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/362 `/scratch/stefan/7930160/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1) `REAL300000082343.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082343 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 88, 88, 192, 192, 192, 192, 192, 192, 192, 192, 192, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 192, 192, 192, 1, 1, 1, 1, 1, 1] 192 rigid atoms, others: [32, 1, 34, 35, 36, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 293 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: REAL300000082343 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 192, 192, 192, 192, 192, 192, 188, 192, 192, 48, 48, 48, 48, 1, 1, 1, 192, 192, 192, 192, 192, 192] 192 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 349 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082343 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082343 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082343/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082343/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082343 Building REAL300000082344 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082344' /scratch/stefan/7930160/working/building/REAL300000082344 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082344 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082344/0 /scratch/stefan/7930160/working/building/REAL300000082344 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/363 `/scratch/stefan/7930160/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2COC3=CC(Cl)=CC(Cl)=C32)=CC=C1F) `REAL300000082344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082344 none O=C([O-])C1=CC(NN=C2COC3=CC(Cl)=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 42, 42, 43, 9, 1, 1, 1, 1, 43, 43] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082344 none O=C([O-])C1=CC(NN=C2COC3=CC(Cl)=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 43, 42, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 11, 43, 43, 43, 43, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082344 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082344 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082344/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082344 Building REAL300000082345 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082345' /scratch/stefan/7930160/working/building/REAL300000082345 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082345 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082345/0 /scratch/stefan/7930160/working/building/REAL300000082345 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/364 `/scratch/stefan/7930160/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC(Br)=C21) `REAL300000082345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082345 none CC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC(Br)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 49 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: REAL300000082345 none CC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC(Br)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 6, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082345 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082345 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082345/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082345 Building REAL300000082346 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082346' /scratch/stefan/7930160/working/building/REAL300000082346 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082346 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082346/0 /scratch/stefan/7930160/working/building/REAL300000082346 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/365 `/scratch/stefan/7930160/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2COCC2=C1) `REAL300000082346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082346 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [11, 1, 11, 11, 59, 152, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 59, 152, 152, 152, 1, 1, 1, 1, 1, 1, 1] 152 rigid atoms, others: [32, 1, 34, 35, 36, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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: REAL300000082346 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 152, 152, 152, 152, 152, 152, 152, 152, 47, 47, 47, 11, 1, 1, 1, 152, 152, 152, 152, 152, 152, 152] 152 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082346 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082346 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082346/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082346 Building REAL300000082347 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082347' /scratch/stefan/7930160/working/building/REAL300000082347 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082347 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082347/0 /scratch/stefan/7930160/working/building/REAL300000082347 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/366 `/scratch/stefan/7930160/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC(F)F)C=C1C) `REAL300000082347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082347 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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: [75, 75, 75, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 154, 201, 201, 75, 37, 74, 75, 75, 75, 75, 27, 6, 1, 1, 1, 201, 75, 75, 75, 75] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082347 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 12, 12, 35, 75, 75, 75, 75, 75, 75, 107, 107, 75, 1, 1, 9, 38, 38, 1, 1, 1, 2, 2, 2, 1, 12, 35, 75, 75, 75, 38, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 35, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082347 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082347 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082347/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082347 Building REAL300000082348 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082348' /scratch/stefan/7930160/working/building/REAL300000082348 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082348 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082348/0 /scratch/stefan/7930160/working/building/REAL300000082348 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/367 `/scratch/stefan/7930160/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2Cl)=CC=C1F) `REAL300000082348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082348 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 30, 8, 1, 1, 1, 67, 67] 67 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082348 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 47, 47, 67, 67, 47, 53, 67, 67, 67, 1, 1, 1, 1, 1, 13, 47, 67, 67, 67, 1, 1] 67 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082348 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082348 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082348/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082348 Building REAL300000082349 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082349' /scratch/stefan/7930160/working/building/REAL300000082349 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082349 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082349/0 /scratch/stefan/7930160/working/building/REAL300000082349 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/368 `/scratch/stefan/7930160/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1N1C=NC=N1) `REAL300000082349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082349 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 123, 123, 79, 91, 152, 152, 152, 134, 123, 123, 123, 123, 56, 11, 1, 1, 1, 123, 123, 152, 152] 160 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082349 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 54, 123, 123, 122, 122, 123, 123, 134, 134, 123, 1, 1, 1, 1, 8, 8, 8, 8, 2, 2, 2, 1, 10, 54, 123, 123, 123, 1, 1, 8, 8] 160 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 17, 18, 19, 20, 28] set([5, 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: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082349 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 13, 13, 80, 148, 148, 148, 149, 148, 148, 160, 160, 148, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 80, 148, 148, 148, 8, 8, 1, 1] 160 rigid atoms, others: [37, 19, 20, 21, 22, 23, 24, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082349 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082349 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082349/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082349 Building REAL300000082350 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082350' /scratch/stefan/7930160/working/building/REAL300000082350 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082350 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082350/0 /scratch/stefan/7930160/working/building/REAL300000082350 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/369 `/scratch/stefan/7930160/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082350 none COC1=CC=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 43, 115, 115, 114, 114, 115, 115, 160, 160, 115, 1, 1, 10, 10, 10, 6, 5, 6, 6, 1, 1, 8, 43, 115, 115, 115, 1, 1] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082350 none COC1=CC=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 84, 178, 178, 178, 178, 178, 178, 201, 201, 178, 6, 6, 3, 3, 3, 1, 1, 1, 1, 6, 6, 19, 84, 178, 178, 178, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082350 none COC1=CC=CC=C1C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 178, 178, 161, 178, 178, 115, 115, 115, 115, 48, 48, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 115, 115, 201, 201, 201, 178, 178, 178, 178, 115, 115, 48, 9, 1, 1, 1, 115, 115] 201 rigid atoms, others: [38, 39, 40, 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, 41, 42]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082350 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082350 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082350/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082350 Building REAL300000082351 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082351' /scratch/stefan/7930160/working/building/REAL300000082351 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082351 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082351/0 /scratch/stefan/7930160/working/building/REAL300000082351 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/370 `/scratch/stefan/7930160/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)=C1) `REAL300000082351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082351 none CC1=CC(C)=CC(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 41, 78, 78, 78, 78, 78, 78, 82, 82, 78, 1, 1, 3, 3, 3, 3, 1, 3, 3, 3, 3, 1, 1, 10, 41, 78, 79, 78, 1, 1, 3] 111 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 43, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 44]) 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: REAL300000082351 none CC1=CC(C)=CC(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 15, 60, 111, 111, 111, 111, 111, 111, 111, 111, 111, 3, 3, 1, 2, 2, 2, 1, 2, 2, 2, 1, 3, 3, 12, 60, 111, 111, 111, 3, 3, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 34, 26, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082351 none CC1=CC(C)=CC(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 73, 111, 111, 111, 56, 54, 76, 76, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 76, 76, 111, 111, 111, 111, 79, 111, 111, 111, 111, 76, 76, 53, 11, 1, 1, 1, 76, 76, 111] 111 rigid atoms, others: [39, 40, 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, 38, 42, 43, 44]) total number of confs: 354 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082351 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082351 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082351/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082351 Building REAL300000082352 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082352' /scratch/stefan/7930160/working/building/REAL300000082352 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082352 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082352/0 /scratch/stefan/7930160/working/building/REAL300000082352 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/371 `/scratch/stefan/7930160/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1) `REAL300000082352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082352 none COC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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, 62, 96, 62, 62, 62, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 96, 96, 96, 62, 62, 29, 9, 1, 1, 1, 62] 96 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, 32, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082352 none COC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 32, 62, 62, 62, 62, 62, 62, 68, 68, 62, 1, 10, 10, 10, 1, 1, 6, 31, 62, 62, 62, 1] 96 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 21, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082352 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082352 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082352/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082352 Building REAL300000082353 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082353' /scratch/stefan/7930160/working/building/REAL300000082353 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082353 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082353/0 /scratch/stefan/7930160/working/building/REAL300000082353 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/372 `/scratch/stefan/7930160/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300000082353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082353 none CC(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 27, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 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: REAL300000082353 none CC(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 201, 201, 177, 201, 201, 201, 118, 118, 118, 118, 41, 41, 1, 1, 1, 201, 201, 200, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082353 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082353 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082353/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082353 Building REAL300000082354 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082354' /scratch/stefan/7930160/working/building/REAL300000082354 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082354 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082354/0 /scratch/stefan/7930160/working/building/REAL300000082354 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/373 `/scratch/stefan/7930160/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082354 none COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 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, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 113, 201, 201, 113, 51, 108, 9, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 51, 51, 51, 51, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 995 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082354 none COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 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, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 9, 9, 9, 23, 23, 23, 23, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 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/7930160/working/building/REAL300000082354 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082354 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082354/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082354 Building REAL300000082355 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082355' /scratch/stefan/7930160/working/building/REAL300000082355 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082355 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082355/0 /scratch/stefan/7930160/working/building/REAL300000082355 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/374 `/scratch/stefan/7930160/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=CC=C1) `REAL300000082355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082355 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [15, 4, 15, 81, 81, 181, 181, 181, 181, 180, 181, 181, 181, 181, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 181, 181, 181, 4, 4, 4, 4, 1, 1, 1, 1, 1] 181 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 292 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: REAL300000082355 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [61, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 147, 156, 181, 181, 172, 181, 181, 61, 61, 61, 61, 1, 1, 1, 156, 156, 156, 156, 181, 181, 181, 181, 181] 181 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 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: 718 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082355 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082355 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082355/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082355 Building REAL300000082356 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082356' /scratch/stefan/7930160/working/building/REAL300000082356 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082356 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082356/0 /scratch/stefan/7930160/working/building/REAL300000082356 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/375 `/scratch/stefan/7930160/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C3C=NC(Br)=CN23)=CC=C1F) `REAL300000082356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082356 none O=C([O-])C1=CC(NN=CC2=CN=C3C=NC(Br)=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'N.pl3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 159, 160, 159, 159, 80, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 80, 12, 1, 1, 1, 159, 159] 160 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082356 none O=C([O-])C1=CC(NN=CC2=CN=C3C=NC(Br)=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'N.pl3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 17, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 60, 60, 159, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 12, 60, 159, 159, 159, 1, 1] 160 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082356 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082356 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082356/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082356 Building REAL300000082357 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082357' /scratch/stefan/7930160/working/building/REAL300000082357 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082357 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082357/0 /scratch/stefan/7930160/working/building/REAL300000082357 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/376 `/scratch/stefan/7930160/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)=O)C=C1) `REAL300000082357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082357 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 105, 105, 105, 105, 105, 105, 129, 129, 105, 1, 1, 1, 1, 1, 12, 12, 1, 1, 6, 6, 6, 31, 105, 105, 105, 1, 1, 13, 13, 13, 1, 1] 167 rigid atoms, others: [1, 35, 36, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) 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: REAL300000082357 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(S(C)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 105, 105, 45, 105, 167, 167, 105, 105, 41, 41, 41, 10, 1, 1, 1, 105, 105, 167, 167, 167, 105, 105] 167 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 619 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082357 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082357 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082357/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082357 Building REAL300000082358 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082358' /scratch/stefan/7930160/working/building/REAL300000082358 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082358 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082358/0 /scratch/stefan/7930160/working/building/REAL300000082358 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/377 `/scratch/stefan/7930160/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F) `REAL300000082358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082358 none CC1=CC=CN=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 104, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 51, 51, 51, 201, 201, 201, 201, 201, 201, 104, 104, 51, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 583 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082358 none CC1=CC=CN=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 8, 19, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 8, 19, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082358 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082358 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082358/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082358 Building REAL300000082359 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082359' /scratch/stefan/7930160/working/building/REAL300000082359 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082359 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082359/0 /scratch/stefan/7930160/working/building/REAL300000082359 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/378 `/scratch/stefan/7930160/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1OC(F)F) `REAL300000082359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082359 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 85, 85, 85, 85, 85, 85, 118, 118, 85, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 9, 9, 9, 37, 85, 85, 85, 1, 1, 1, 36] 201 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 402 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082359 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 85, 85, 69, 85, 85, 85, 85, 173, 201, 201, 29, 29, 29, 7, 1, 1, 1, 85, 85, 85, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 491 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082359 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082359 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082359/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082359 Building REAL300000082360 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082360' /scratch/stefan/7930160/working/building/REAL300000082360 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082360 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082360/0 /scratch/stefan/7930160/working/building/REAL300000082360 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/379 `/scratch/stefan/7930160/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F) `REAL300000082360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082360 none O=C([O-])C1=CC(N=NC2CCCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 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: [50, 32, 50, 32, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 32, 32] 63 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082360 none O=C([O-])C1=CC(N=NC2CCCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 32, 32, 32, 32, 32, 32, 63, 63, 32, 32, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 63, 63, 63, 63, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082360 none O=C([O-])C1=CC(N=NC2CCCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 63, 63, 63, 63, 63, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 94 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082360 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082360 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082360/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082360 Building REAL300000082361 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082361' /scratch/stefan/7930160/working/building/REAL300000082361 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082361 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082361/0 /scratch/stefan/7930160/working/building/REAL300000082361 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/380 `/scratch/stefan/7930160/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082361 none C[N@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 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, 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: [48, 48, 48, 48, 68, 74, 74, 68, 74, 74, 38, 28, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 68, 68, 74, 74, 68, 74, 74, 48, 48, 39, 39, 39, 39, 39, 39, 28, 28, 1, 1, 1] 74 rigid atoms, others: [48, 49, 47, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082361 none C[N@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 9, 13, 15, 15, 15, 19, 55, 55, 74, 74, 74, 74, 74, 74, 74, 74, 74, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 15, 15, 15, 19, 19, 74, 74, 74] 74 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082361 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082361/1 /scratch/stefan/7930160/working/building/REAL300000082361 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/381 `/scratch/stefan/7930160/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082361.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082361 none C[N@@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 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, 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: [44, 44, 44, 44, 64, 71, 71, 71, 71, 71, 34, 25, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 64, 64, 71, 71, 71, 71, 71, 44, 44, 34, 34, 34, 34, 34, 34, 24, 25, 1, 1, 1] 71 rigid atoms, others: [48, 49, 47, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082361 none C[N@@H+](CC1=CC=CC=C1)CC(C)(C)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 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, 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, 4, 9, 1, 1, 1, 1, 1, 1, 1, 9, 13, 15, 15, 15, 19, 55, 55, 71, 71, 71, 71, 71, 71, 71, 71, 71, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 15, 15, 15, 19, 19, 71, 71, 71] 71 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082361 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082361 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082361/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082361/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082361 Building REAL300000082362 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082362' /scratch/stefan/7930160/working/building/REAL300000082362 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082362 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082362/0 /scratch/stefan/7930160/working/building/REAL300000082362 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/382 `/scratch/stefan/7930160/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=NC(N)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082362 none COC1=NC=NC(N)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 4, 7, 7, 7, 4, 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, 79, 79, 79, 58, 79, 79, 79, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 60, 79, 79, 52, 11, 1, 1, 1] 82 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082362 none COC1=NC=NC(N)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 4, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 79, 79, 79, 79, 79, 79, 82, 82, 79, 3, 3, 3, 1, 2, 2, 11, 41, 79, 79, 79] 82 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([0, 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082362 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082362 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082362/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082362 Building REAL300000082363 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082363' /scratch/stefan/7930160/working/building/REAL300000082363 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082363 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082363/0 /scratch/stefan/7930160/working/building/REAL300000082363 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/383 `/scratch/stefan/7930160/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C) `REAL300000082363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082363 none CCCCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 131, 67, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 201, 201, 201, 201, 201, 198, 198, 131, 131, 29, 29, 29, 29, 1, 1, 1, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082363 none CCCCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 45, 21, 5, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 29, 29, 29, 44, 44, 29, 1, 1, 1, 52, 52, 52, 52, 52, 45, 45, 21, 21, 1, 1, 1, 1, 29, 29, 29, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 20, 21, 22] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082363 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082363 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082363/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082363 Building REAL300000082364 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082364' /scratch/stefan/7930160/working/building/REAL300000082364 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082364 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082364/0 /scratch/stefan/7930160/working/building/REAL300000082364 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/384 `/scratch/stefan/7930160/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C(C)C)C=C1) `REAL300000082364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082364 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 100, 100, 100, 100, 175, 175, 174, 175, 201, 201, 175, 175, 101, 101, 101, 101, 41, 8, 1, 1, 1, 101, 101, 101, 175, 175, 201, 201, 201, 201, 201, 201, 201, 175, 175] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082364 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 43, 101, 101, 101, 101, 101, 101, 158, 158, 101, 1, 1, 1, 1, 3, 3, 2, 2, 7, 7, 3, 3, 2, 2, 2, 1, 8, 42, 101, 101, 100, 2, 2, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 17, 18, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082364 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 15, 15, 78, 175, 175, 175, 175, 175, 175, 199, 199, 175, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 3, 3, 3, 3, 15, 78, 175, 175, 175, 3, 3, 3, 1, 1, 4, 5, 5, 5, 4, 4, 4, 1, 1] 201 rigid atoms, others: [51, 41, 42, 50, 19, 20, 21, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 436 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082364 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082364 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082364/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082364 Building REAL300000082365 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082365' /scratch/stefan/7930160/working/building/REAL300000082365 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082365 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082365/0 /scratch/stefan/7930160/working/building/REAL300000082365 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/385 `/scratch/stefan/7930160/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=N2)N=C1) `REAL300000082365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082365 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 57, 176, 176, 176, 176, 176, 176, 201, 201, 176, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 10, 10, 10, 56, 176, 176, 176, 2, 2, 2, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 40, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 412 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082365 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 176, 176, 176, 176, 201, 201, 201, 201, 201, 176, 176, 50, 50, 50, 8, 1, 1, 1, 176, 176, 176, 201, 201, 201, 201, 176] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082365 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=N2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7] 0 hydrogens 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, 6, 28, 28, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 112, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 6] 201 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 410 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082365 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082365 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082365/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082365 Building REAL300000082366 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082366' /scratch/stefan/7930160/working/building/REAL300000082366 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082366 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082366/0 /scratch/stefan/7930160/working/building/REAL300000082366 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/386 `/scratch/stefan/7930160/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCSC3=CC=C(Cl)C=C32)=CC=C1F) `REAL300000082366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082366 none O=C([O-])C1=CC(NN=C2CCCSC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 34, 34, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082366 none O=C([O-])C1=CC(NN=C2CCCSC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 1, 1, 1, 1, 1, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082366 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082366 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082366/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082366 Building REAL300000082367 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082367' /scratch/stefan/7930160/working/building/REAL300000082367 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082367 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082367/0 /scratch/stefan/7930160/working/building/REAL300000082367 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/387 `/scratch/stefan/7930160/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082367 none COC1=CC=C2CCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [66, 46, 46, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 67, 67, 67, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1, 46] 67 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) 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: REAL300000082367 none COC1=CC=C2CCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 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, 1, 1, 1, 1, 9, 46, 46, 46, 46, 46, 46, 59, 59, 46, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 36, 26, 27, 28, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082367 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082367 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082367/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082367 Building REAL300000082368 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082368' /scratch/stefan/7930160/working/building/REAL300000082368 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082368 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082368/0 /scratch/stefan/7930160/working/building/REAL300000082368 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/388 `/scratch/stefan/7930160/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082368 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 42, 69, 69, 69, 42, 31, 10, 1, 1, 1, 42, 42] 69 rigid atoms, others: [33, 34, 35, 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, 36, 37]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082368 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 14, 42, 42, 42, 42, 42, 42, 69, 69, 42, 1, 1, 3, 3, 3, 1, 4, 14, 42, 42, 42, 1, 1] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 37, 30, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082368 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082368 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082368/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082368 Building REAL300000082369 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082369' /scratch/stefan/7930160/working/building/REAL300000082369 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082369 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082369/0 /scratch/stefan/7930160/working/building/REAL300000082369 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/389 `/scratch/stefan/7930160/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2[O-])=CC=C1F) `REAL300000082369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082369 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 10, 4, 1, 1, 1, 19, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082369 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 14, 14, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 8, 14, 19, 19, 19, 1, 1] 19 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: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082369 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082369/1 /scratch/stefan/7930160/working/building/REAL300000082369 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/390 `/scratch/stefan/7930160/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2O)=CC=C1F) `REAL300000082369.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082369 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 26, 6, 1, 1, 1, 2, 51, 51] 102 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082369 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 10, 40, 51, 51, 51, 102, 1, 1] 102 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 189 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082369 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082369 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082369/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082369/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082369 Building REAL300000082370 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082370' /scratch/stefan/7930160/working/building/REAL300000082370 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082370 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082370/0 /scratch/stefan/7930160/working/building/REAL300000082370 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/391 `/scratch/stefan/7930160/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC(F)=CC=C32)=CC=C1F) `REAL300000082370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082370 none O=C([O-])C1=CC(NN=C2CCCC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 54 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: REAL300000082370 none O=C([O-])C1=CC(NN=C2CCCC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082370 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082370 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082370/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082370 Building REAL300000082371 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082371' /scratch/stefan/7930160/working/building/REAL300000082371 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082371 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082371/0 /scratch/stefan/7930160/working/building/REAL300000082371 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/392 `/scratch/stefan/7930160/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CC3(CCCC3)OC3=CC=CC=C32)=CC=C1F) `REAL300000082371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082371 none O=C([O-])C1=CC(NN=C2CC3(CCCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 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, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 42, 43, 22, 23, 24, 25, 26, 27]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082371 none O=C([O-])C1=CC(NN=C2CC3(CCCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082371 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082371 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082371/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082371 Building REAL300000082372 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082372' /scratch/stefan/7930160/working/building/REAL300000082372 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082372 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082372/0 /scratch/stefan/7930160/working/building/REAL300000082372 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/393 `/scratch/stefan/7930160/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCCC2)=CC=C1F) `REAL300000082372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082372 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 21, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15] 21 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 51 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: REAL300000082372 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 49, 50, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082372 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 21 rigid atoms, others: [48, 45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50]) total number of confs: 33 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082372 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082372 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082372/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082372 Building REAL300000082373 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082373' /scratch/stefan/7930160/working/building/REAL300000082373 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082373 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082373/0 /scratch/stefan/7930160/working/building/REAL300000082373 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/394 `/scratch/stefan/7930160/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1) `REAL300000082373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082373 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 10, 1, 1, 1, 40, 40, 40, 40] 40 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 66 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: REAL300000082373 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 40, 40, 40, 1, 1, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 36, 37, 38, 39] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082373 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082373 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082373/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082373 Building REAL300000082374 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082374' /scratch/stefan/7930160/working/building/REAL300000082374 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082374 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082374/0 /scratch/stefan/7930160/working/building/REAL300000082374 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/395 `/scratch/stefan/7930160/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC3(CCOCC3)CC2)=CC=C1F) `REAL300000082374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082374 none O=C([O-])C1=CC(N=NC2CCC3(CCOCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 41, 42, 19, 20, 21, 22, 23]) 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: REAL300000082374 none O=C([O-])C1=CC(N=NC2CCC3(CCOCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082374 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082374 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082374/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082374 Building REAL300000082375 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082375' /scratch/stefan/7930160/working/building/REAL300000082375 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082375 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082375/0 /scratch/stefan/7930160/working/building/REAL300000082375 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/396 `/scratch/stefan/7930160/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2C)C=C1) `REAL300000082375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082375 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 93, 93, 93, 93, 93, 93, 109, 109, 93, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 31, 93, 93, 93, 1, 1, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [1, 34, 33, 40, 41, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 230 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082375 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 93, 93, 47, 63, 201, 199, 201, 201, 201, 93, 93, 40, 40, 40, 8, 1, 1, 1, 93, 93, 201, 201, 201, 199, 196, 93, 93] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 495 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082375 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 13, 17, 95, 200, 201, 201, 201, 197, 195, 201, 201, 194, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 17, 17, 85, 200, 200, 192, 5, 5, 1, 1, 2, 2, 2, 5, 5] 201 rigid atoms, others: [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, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 448 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082375 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082375 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082375/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082375 Building REAL300000082376 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082376' /scratch/stefan/7930160/working/building/REAL300000082376 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082376 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082376/0 /scratch/stefan/7930160/working/building/REAL300000082376 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/397 `/scratch/stefan/7930160/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)C[NH+](C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082376 none CC1CC(C)C[NH+](C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 5, 5] 31 rigid atoms, others: [45, 43, 6, 39, 8, 9, 10, 11, 12, 13, 46, 44, 48, 40, 14, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51, 52, 53]) total number of confs: 43 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082376 none CC1CC(C)C[NH+](C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 33, 52, 53, 26, 38, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082376 none CC1CC(C)C[NH+](C2CCCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 31, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 31, 31] 31 rigid atoms, others: [51, 49, 50, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53]) total number of confs: 80 number of broken/clashed sets: 29 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082376 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082376 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082376/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082376 Building REAL300000082377 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082377' /scratch/stefan/7930160/working/building/REAL300000082377 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082377 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082377/0 /scratch/stefan/7930160/working/building/REAL300000082377 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/398 `/scratch/stefan/7930160/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C) `REAL300000082377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082377 none CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 5, 21, 21, 62, 62, 62, 62, 62, 62, 78, 78, 62, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 18, 18, 18, 7, 7, 7, 7, 7, 5, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 111 rigid atoms, others: [2, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 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: REAL300000082377 none CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [34, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 62, 62, 62, 62, 62, 62, 85, 85, 111, 111, 111, 111, 38, 38, 38, 38, 38, 37, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 111, 111, 111, 111, 111, 111, 111, 111, 111] 111 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 14, 36] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 390 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082377 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082377 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082377/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082377 Building REAL300000082378 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082378' /scratch/stefan/7930160/working/building/REAL300000082378 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082378 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082378/0 /scratch/stefan/7930160/working/building/REAL300000082378 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/399 `/scratch/stefan/7930160/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3=CSC=C3)S2)=CC=C1F) `REAL300000082378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082378 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CSC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 117, 123, 117, 117, 48, 8, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 117, 117, 117, 117, 117, 48, 8, 1, 4, 4, 4, 117, 117] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082378 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CSC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 56, 56, 117, 117, 117, 117, 201, 201, 201, 201, 117, 1, 1, 1, 1, 1, 13, 56, 117, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082378 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CSC=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 105, 22, 22, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 201, 201, 201, 201, 201, 105, 22, 4, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 395 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082378 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082378 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082378/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082378 Building REAL300000082379 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082379' /scratch/stefan/7930160/working/building/REAL300000082379 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082379 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082379/0 /scratch/stefan/7930160/working/building/REAL300000082379 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/400 `/scratch/stefan/7930160/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)N=C2)=CC=C1F) `REAL300000082379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082379 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 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: [118, 118, 118, 118, 118, 49, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 118, 118, 117, 117, 118, 49, 8, 1, 1, 6, 6, 6, 1, 118, 118] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34]) 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: REAL300000082379 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 13, 58, 58, 118, 118, 118, 118, 201, 201, 201, 201, 118, 118, 1, 1, 1, 1, 1, 13, 58, 118, 118, 201, 201, 201, 118, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082379 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 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, 201, 201, 94, 18, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 94, 18, 6, 6, 1, 1, 1, 6, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082379 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082379 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082379/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082379 Building REAL300000082380 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082380' /scratch/stefan/7930160/working/building/REAL300000082380 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082380 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082380/0 /scratch/stefan/7930160/working/building/REAL300000082380 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/401 `/scratch/stefan/7930160/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CC3(CCC3)OC3=CC=CC=C32)=CC=C1F) `REAL300000082380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082380 none O=C([O-])C1=CC(NN=C2CC3(CCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 39, 40, 21, 22, 23, 24, 25, 26]) total number of confs: 57 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082380 none O=C([O-])C1=CC(NN=C2CC3(CCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082380 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082380 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082380/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082380 Building REAL300000082381 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082381' /scratch/stefan/7930160/working/building/REAL300000082381 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082381 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082381/0 /scratch/stefan/7930160/working/building/REAL300000082381 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/402 `/scratch/stefan/7930160/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C2=CC=CC=C2)C1) `REAL300000082381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082381 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 74, 74, 48, 74, 74, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 48, 48, 48, 74, 74, 74, 74, 74, 48, 48] 74 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082381 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 48, 48, 48, 48, 48, 48, 74, 74, 48, 1, 1, 1, 4, 4, 2, 4, 4, 1, 2, 2, 2, 1, 1, 1, 1, 48, 48, 48, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 74 rigid atoms, others: [0, 1, 2, 3, 4, 37, 43, 44, 16, 17, 18, 35, 24, 36, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082381 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 28, 28, 74, 74, 74, 74, 74, 74, 74, 74, 74, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 74, 74, 74, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 74 rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082381 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082381 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082381/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082381 Building REAL300000082382 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082382' /scratch/stefan/7930160/working/building/REAL300000082382 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082382 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082382/0 /scratch/stefan/7930160/working/building/REAL300000082382 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/403 `/scratch/stefan/7930160/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1) `REAL300000082382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082382 none COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 76, 119, 76, 76, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 76, 76, 119, 119, 119, 76, 29, 9, 1, 1, 1, 76, 76] 119 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000082382 none COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [10, 10, 1, 10, 1, 1, 1, 1, 7, 7, 41, 76, 76, 76, 76, 76, 76, 78, 78, 76, 1, 1, 11, 10, 10, 1, 7, 41, 76, 76, 76, 1, 1] 119 rigid atoms, others: [32, 2, 4, 5, 6, 7, 20, 21, 25, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082382 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082382 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082382/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082382 Building REAL300000082383 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082383' /scratch/stefan/7930160/working/building/REAL300000082383 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082383 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082383/0 /scratch/stefan/7930160/working/building/REAL300000082383 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/404 `/scratch/stefan/7930160/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=C([O-])C(F)=C2)=CC=C1F) `REAL300000082383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082383 none O=C([O-])C1=CC(NN=CC2=CC(F)=C([O-])C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 22, 6, 1, 1, 27, 27] 27 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082383 none O=C([O-])C1=CC(NN=CC2=CC(F)=C([O-])C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 19, 19, 27, 27, 27, 19, 19, 27, 27, 27, 1, 1, 1, 1, 1, 6, 19, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082383 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082383/1 /scratch/stefan/7930160/working/building/REAL300000082383 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/405 `/scratch/stefan/7930160/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=C(O)C(F)=C2)=CC=C1F) `REAL300000082383.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082383 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(O)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 59, 59, 60, 32, 8, 1, 2, 1, 60, 60] 120 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 26, 28, 29]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082383 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(O)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 12, 43, 43, 62, 62, 62, 44, 45, 62, 62, 62, 1, 1, 1, 1, 1, 12, 43, 62, 124, 62, 1, 1] 124 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: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082383 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082383 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082383/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082383/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082383 Building REAL300000082384 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082384' /scratch/stefan/7930160/working/building/REAL300000082384 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082384 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082384/0 /scratch/stefan/7930160/working/building/REAL300000082384 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/406 `/scratch/stefan/7930160/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC([O-])=CC=C2[N+](=O)[O-])=CC=C1F) `REAL300000082384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082384 none O=C([O-])C1=CC(NN=CC2=CC([O-])=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 38, 38, 38, 38, 27, 7, 1, 1, 1, 38, 38] 38 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082384 none O=C([O-])C1=CC(NN=CC2=CC([O-])=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 5, 20, 38, 38, 38, 1, 1] 38 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082384 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082384/1 /scratch/stefan/7930160/working/building/REAL300000082384 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/407 `/scratch/stefan/7930160/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2[N+](=O)[O-])=CC=C1F) `REAL300000082384.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082384 none O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [87, 87, 87, 87, 87, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 87, 87, 87, 87, 87, 33, 7, 1, 2, 1, 1, 87, 87] 174 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082384 none O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 12, 63, 63, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 12, 63, 87, 174, 87, 87, 1, 1] 174 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082384 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082384 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082384/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082384/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082384 Building REAL300000082385 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082385' /scratch/stefan/7930160/working/building/REAL300000082385 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082385 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082385/0 /scratch/stefan/7930160/working/building/REAL300000082385 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/408 `/scratch/stefan/7930160/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082385 none CC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [54, 9, 54, 127, 155, 155, 155, 155, 155, 155, 155, 155, 155, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 54, 54, 127, 127, 155, 155, 155, 155, 1, 1, 1] 155 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 546 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: REAL300000082385 none CC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 64, 64, 155, 155, 155, 155, 155, 155, 155, 155, 155, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 155, 155, 155] 155 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 11, 12, 34, 31] set([0, 1, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082385 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082385 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082385/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082385 Building REAL300000082386 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082386' /scratch/stefan/7930160/working/building/REAL300000082386 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082386 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082386/0 /scratch/stefan/7930160/working/building/REAL300000082386 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/409 `/scratch/stefan/7930160/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2(C[NH+]3CCOCC3)CCCCC2)=CC=C1F) `REAL300000082386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(C[NH+]3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [35, 33, 35, 33, 33, 25, 25, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 51 rigid atoms, others: [49, 8, 9, 10, 43, 44, 45, 46, 47, 48, 40, 18, 19, 20, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51]) total number of confs: 93 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: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(C[NH+]3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 23, 32, 35, 51, 51, 51, 51, 51, 51, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 23, 23, 35, 35, 51, 51, 51, 51, 51, 51, 51, 51, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 50, 51, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(C[NH+]3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 49, 49, 17, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 51, 51, 51, 51, 51, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 51, 51] 51 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082386 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082386/1 /scratch/stefan/7930160/working/building/REAL300000082386 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/410 `/scratch/stefan/7930160/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2(CN3CCOCC3)CCCCC2)=CC=C1F) `REAL300000082386.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(CN3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 38, 37, 37, 17, 17, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 38 rigid atoms, others: [41, 39, 8, 9, 10, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50]) total number of confs: 79 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(CN3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 22, 37, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 21, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 38 rigid atoms, others: [1, 3, 4, 5, 6, 49, 50, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082386 none O=C([O-])C1=CC(N=NCC2(CN3CCOCC3)CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 21, 21, 6, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 38, 38] 38 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082386 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082386 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082386/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082386/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082386 Building REAL300000082387 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082387' /scratch/stefan/7930160/working/building/REAL300000082387 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082387 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082387/0 /scratch/stefan/7930160/working/building/REAL300000082387 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/411 `/scratch/stefan/7930160/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C(C)C)S1) `REAL300000082387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082387 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 10, 10, 54, 135, 135, 135, 135, 135, 135, 174, 174, 135, 1, 1, 1, 1, 1, 1, 12, 12, 1, 10, 10, 10, 54, 135, 135, 135, 2, 2, 2, 12, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 22] set([0, 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, 38, 39]) total number of confs: 455 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082387 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N=C(C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 135, 135, 135, 135, 135, 201, 201, 135, 43, 43, 43, 8, 1, 1, 1, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 546 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082387 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082387 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082387/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082387 Building REAL300000082388 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082388' /scratch/stefan/7930160/working/building/REAL300000082388 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082388 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082388/0 /scratch/stefan/7930160/working/building/REAL300000082388 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/412 `/scratch/stefan/7930160/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C) `REAL300000082388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082388 none CC1=CC=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 73, 73, 16, 3, 1, 1, 1, 1, 1, 1, 1, 16, 16, 46, 74, 74, 74, 74, 74, 74, 91, 91, 74, 73, 73, 73, 73, 73, 73, 73, 73, 3, 3, 1, 1, 1, 1, 1, 46, 74, 74, 74, 73, 73, 73, 73] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 545 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082388 none CC1=CC=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 51, 73, 73, 55, 73, 73, 12, 12, 69, 126, 126, 126, 126, 126, 126, 147, 147, 126, 1, 1, 1, 2, 2, 2, 1, 1, 51, 51, 73, 73, 73, 73, 73, 69, 126, 126, 126, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 616 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082388 none CC1=CC=C(C(CC2=CC=CC=C2)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 126, 126, 22, 22, 21, 62, 74, 74, 67, 74, 74, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 126, 126, 126, 126, 126, 126, 126, 126, 62, 62, 74, 74, 74, 74, 74, 5, 1, 1, 1, 126, 126, 126, 126] 201 rigid atoms, others: [41, 42, 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, 40, 44, 45, 46, 47]) total number of confs: 853 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082388 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082388 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082388/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082388 Building REAL300000082389 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082389' /scratch/stefan/7930160/working/building/REAL300000082389 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082389 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082389/0 /scratch/stefan/7930160/working/building/REAL300000082389 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/413 `/scratch/stefan/7930160/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC=C(F)C=C32)=CC=C1F) `REAL300000082389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082389 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 43 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: REAL300000082389 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082389 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082389 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082389/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082389 Building REAL300000082390 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082390' /scratch/stefan/7930160/working/building/REAL300000082390 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082390 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082390/0 /scratch/stefan/7930160/working/building/REAL300000082390 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/414 `/scratch/stefan/7930160/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082390 none COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [157, 100, 100, 100, 100, 100, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 100, 100, 100, 158, 157, 157, 157, 100, 100, 100, 100, 30, 10, 1, 1, 1, 100, 158, 158, 158] 175 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) 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: REAL300000082390 none COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 100, 100, 100, 100, 100, 100, 138, 138, 100, 1, 1, 1, 3, 3, 3, 3, 1, 2, 2, 2, 9, 40, 100, 100, 100, 1, 3, 3, 3] 175 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082390 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082390 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082390/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082390 Building REAL300000082391 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082391' /scratch/stefan/7930160/working/building/REAL300000082391 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082391 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082391/0 /scratch/stefan/7930160/working/building/REAL300000082391 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/415 `/scratch/stefan/7930160/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(F)=C1) `REAL300000082391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082391 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [11, 1, 11, 11, 61, 163, 163, 163, 163, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 163, 163, 163, 1, 1, 2, 2, 2, 1] 163 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) 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: REAL300000082391 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 163, 163, 163, 163, 163, 163, 163, 55, 55, 55, 11, 1, 1, 1, 163, 163, 163, 163, 163, 163] 163 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 243 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082391 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082391 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082391/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082391 Building REAL300000082392 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082392' /scratch/stefan/7930160/working/building/REAL300000082392 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082392 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082392/0 /scratch/stefan/7930160/working/building/REAL300000082392 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/416 `/scratch/stefan/7930160/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082392 none CS(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [80, 35, 80, 35, 68, 68, 35, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 80, 80, 80, 68, 67, 34, 10, 1, 1, 1, 68, 68] 85 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) 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: REAL300000082392 none CS(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 25, 67, 67, 67, 67, 67, 67, 75, 75, 67, 1, 1, 5, 5, 5, 1, 1, 6, 25, 67, 67, 67, 1, 1] 85 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 20, 21, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082392 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082392 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082392/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082392 Building REAL300000082393 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082393' /scratch/stefan/7930160/working/building/REAL300000082393 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082393 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082393/0 /scratch/stefan/7930160/working/building/REAL300000082393 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/417 `/scratch/stefan/7930160/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1) `REAL300000082393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082393 none CC1=C(C)C=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 5, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 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 201 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, 8, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 35, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082393 none CC1=C(C)C=C2OC(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 5, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 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 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, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 13, 13, 13, 13, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082393 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082393/1 /scratch/stefan/7930160/working/building/REAL300000082393 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/418 `/scratch/stefan/7930160/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC(C)=C(C)C=C2O1) `REAL300000082393.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082393 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC(C)=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 37, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 68, 68, 67, 1, 1, 2, 2, 2, 2, 2, 2, 1] 68 rigid atoms, others: [32, 1, 33, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082393 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC(C)=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 67, 67, 67, 67, 67, 67, 68, 67, 67, 67, 37, 37, 37, 10, 1, 1, 1, 67, 67, 68, 68, 68, 68, 68, 68, 68] 68 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082393 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082393 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082393/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082393/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082393 Building REAL300000082394 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082394' /scratch/stefan/7930160/working/building/REAL300000082394 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082394 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082394/0 /scratch/stefan/7930160/working/building/REAL300000082394 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/419 `/scratch/stefan/7930160/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=NC2=CC=CC=C2S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082394 none CC(CC1=NC2=CC=CC=C2S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 6, 37, 107, 201, 201, 201, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 37, 37, 107, 107, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082394 none CC(CC1=NC2=CC=CC=C2S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 7, 7, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082394 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082394 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082394/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082394 Building REAL300000082395 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082395' /scratch/stefan/7930160/working/building/REAL300000082395 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082395 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082395/0 /scratch/stefan/7930160/working/building/REAL300000082395 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/420 `/scratch/stefan/7930160/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C) `REAL300000082395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082395 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 53, 53, 119, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 119, 119, 119, 1, 1, 1, 2, 2, 2] 119 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082395 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 119, 119, 119, 119, 119, 119, 119, 119, 119, 119, 48, 48, 48, 48, 1, 1, 1, 119, 119, 119, 119, 119, 119] 119 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 258 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082395 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082395/1 /scratch/stefan/7930160/working/building/REAL300000082395 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/421 `/scratch/stefan/7930160/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C) `REAL300000082395.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082395 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 69, 69, 69, 1, 1, 1, 2, 2, 2] 69 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082395 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC(Cl)=CC=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [48, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 49, 49, 49, 13, 1, 1, 1, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082395 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082395 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082395/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082395/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082395 Building REAL300000082396 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082396' /scratch/stefan/7930160/working/building/REAL300000082396 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082396 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082396/0 /scratch/stefan/7930160/working/building/REAL300000082396 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/422 `/scratch/stefan/7930160/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=CC=C1)CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082396 none CC(CCC1=CC=CC=C1)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 119, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 131, 131, 131, 131, 201, 200, 201, 201, 201, 201, 201, 201, 201, 39, 39, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37]) total number of confs: 985 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082396 none CC(CCC1=CC=CC=C1)CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 201, 201, 201] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 33, 27, 28, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082396 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082396 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082396/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082396 Building REAL300000082397 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082397' /scratch/stefan/7930160/working/building/REAL300000082397 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082397 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082397/0 /scratch/stefan/7930160/working/building/REAL300000082397 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/423 `/scratch/stefan/7930160/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=C1)OCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082397 none COC1=CC=C2C(=C1)OCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [90, 50, 50, 50, 50, 46, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 91, 91, 91, 50, 50, 50, 50, 50, 10, 1, 1, 1] 91 rigid atoms, others: [32, 33, 34, 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]) 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: REAL300000082397 none COC1=CC=C2C(=C1)OCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 91, 91, 50, 3, 3, 3, 1, 1, 1, 1, 1, 9, 50, 50, 50] 91 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 32, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082397 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082397 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082397/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082397 Building REAL300000082398 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082398' /scratch/stefan/7930160/working/building/REAL300000082398 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082398 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082398/0 /scratch/stefan/7930160/working/building/REAL300000082398 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/424 `/scratch/stefan/7930160/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(O)C=C2C=C1) `REAL300000082398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082398 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(O)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 56, 151, 151, 151, 151, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 151, 151, 151, 1, 1, 1, 2, 1, 1, 1] 302 rigid atoms, others: [32, 1, 34, 36, 37, 38, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 270 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: REAL300000082398 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(O)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 302 conformations in input total number of sets (complete confs): 302 using faster count positions algorithm for large data unique positions, atoms: [50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 51, 51, 51, 11, 1, 1, 1, 151, 151, 151, 302, 151, 151, 151] 302 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 524 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082398 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082398 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082398/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082398 Building REAL300000082399 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082399' /scratch/stefan/7930160/working/building/REAL300000082399 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082399 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082399/0 /scratch/stefan/7930160/working/building/REAL300000082399 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/425 `/scratch/stefan/7930160/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CS3)S2)=CC=C1F) `REAL300000082399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082399 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CS3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 108, 120, 108, 108, 45, 6, 6, 1, 1, 1, 1, 1, 1, 13, 12, 12, 13, 1, 108, 108, 108, 108, 108, 44, 6, 1, 13, 13, 12, 108, 108] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082399 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CS3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 56, 56, 108, 108, 108, 108, 201, 201, 201, 201, 108, 1, 1, 1, 1, 1, 13, 56, 108, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082399 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CS3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 133, 48, 48, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 200, 201, 201, 201, 201, 133, 47, 13, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 444 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082399 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082399 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082399/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082399 Building REAL300000082400 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082400' /scratch/stefan/7930160/working/building/REAL300000082400 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082400 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082400/0 /scratch/stefan/7930160/working/building/REAL300000082400 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/426 `/scratch/stefan/7930160/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Br) `REAL300000082400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082400 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 48, 48, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 113, 113, 84, 113, 113, 113, 113, 113, 48, 13, 1, 1, 1, 113, 113] 113 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082400 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 57, 113, 113, 112, 112, 113, 113, 113, 113, 113, 1, 1, 1, 1, 2, 2, 2, 1, 8, 57, 113, 113, 113, 1, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 24, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082400 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082400 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082400/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082400 Building REAL300000082401 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082401' /scratch/stefan/7930160/working/building/REAL300000082401 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082401 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082401/0 /scratch/stefan/7930160/working/building/REAL300000082401 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/427 `/scratch/stefan/7930160/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCCC3)S2)=CC=C1F) `REAL300000082401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082401 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 122, 87, 87, 46, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 87, 87, 86, 86, 87, 46, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 87, 87] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082401 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 35, 35, 87, 87, 87, 87, 201, 201, 201, 201, 201, 87, 1, 1, 1, 1, 1, 9, 35, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082401 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 163, 54, 53, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 163, 54, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082401 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082401 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082401/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082401 Building REAL300000082402 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082402' /scratch/stefan/7930160/working/building/REAL300000082402 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082402 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082402/0 /scratch/stefan/7930160/working/building/REAL300000082402 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/428 `/scratch/stefan/7930160/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1) `REAL300000082402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082402 none CCOC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 140, 80, 140, 80, 80, 80, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 80, 201, 201, 201, 201, 201, 80, 80, 43, 9, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082402 none CCOC(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 36, 80, 80, 79, 79, 80, 80, 123, 123, 80, 1, 34, 34, 34, 34, 34, 1, 1, 6, 36, 80, 80, 80] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 22, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082402 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082402 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082402/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082402 Building REAL300000082403 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082403' /scratch/stefan/7930160/working/building/REAL300000082403 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082403 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082403/0 /scratch/stefan/7930160/working/building/REAL300000082403 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/429 `/scratch/stefan/7930160/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CCC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082403 none CC(C)C(CCC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 59, 127, 8, 59, 119, 147, 172, 172, 172, 172, 172, 172, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 130, 130, 130, 130, 130, 130, 130, 59, 128, 128, 143, 147, 172, 172, 172, 172, 1, 1, 1] 201 rigid atoms, others: [41, 42, 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, 40]) total number of confs: 1087 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: REAL300000082403 none CC(C)C(CCC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 17, 37, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 64, 64, 172, 172, 172, 172, 172, 172, 190, 190, 172, 38, 38, 38, 38, 38, 37, 38, 17, 5, 5, 3, 3, 1, 1, 1, 1, 172, 172, 172] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 447 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082403 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082403 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082403/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082403 Building REAL300000082404 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082404' /scratch/stefan/7930160/working/building/REAL300000082404 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082404 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082404/0 /scratch/stefan/7930160/working/building/REAL300000082404 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/430 `/scratch/stefan/7930160/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082404 none CC1C[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 56, 56, 101, 101, 101, 101, 101, 101, 101, 101, 101, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 101, 101, 101] 101 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 155 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: REAL300000082404 none CC1C[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 10, 10, 8, 10, 10, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 47, 61, 61, 47, 2, 2, 2, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 1, 1, 1, 47, 47, 47] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 41, 12, 13, 14, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082404 none CC1C[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 47, 47, 47, 47, 92, 101, 101, 94, 101, 101, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 47, 47, 47, 47, 92, 92, 101, 101, 101, 101, 101, 47, 47, 47, 1, 1, 1] 101 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 377 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082404 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082404/1 /scratch/stefan/7930160/working/building/REAL300000082404 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/431 `/scratch/stefan/7930160/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082404.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082404 none CC1C[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 3, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 60, 60, 117, 117, 117, 117, 117, 117, 117, 117, 117, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 11, 11, 11, 117, 117, 117] 117 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 178 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: REAL300000082404 none CC1C[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 11, 11, 9, 11, 11, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 56, 56, 34, 2, 2, 2, 1, 1, 1, 7, 7, 11, 11, 10, 11, 11, 1, 1, 1, 34, 34, 34] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 41, 12, 13, 14, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082404 none CC1C[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 34, 34, 97, 117, 117, 104, 117, 117, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 34, 34, 34, 97, 97, 117, 117, 110, 117, 117, 34, 34, 34, 1, 1, 1] 117 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 428 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082404 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082404 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082404/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082404/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082404 Building REAL300000082405 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082405' /scratch/stefan/7930160/working/building/REAL300000082405 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082405 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082405/0 /scratch/stefan/7930160/working/building/REAL300000082405 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/432 `/scratch/stefan/7930160/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCCC2)C=C1O) `REAL300000082405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082405 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCCC2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 244 conformations in input total number of sets (complete confs): 244 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 47, 87, 87, 87, 87, 87, 87, 95, 95, 87, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 11, 47, 87, 87, 87, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2] 244 rigid atoms, others: [1, 34, 33, 43, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 218 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: REAL300000082405 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCCC2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 244 conformations in input total number of sets (complete confs): 244 using faster count positions algorithm for large data unique positions, atoms: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 87, 87, 66, 87, 122, 122, 122, 122, 87, 87, 87, 24, 24, 24, 6, 1, 1, 1, 87, 87, 122, 122, 122, 122, 122, 122, 122, 122, 87, 174] 244 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 460 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082405 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCCC2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 244 conformations in input total number of sets (complete confs): 244 using faster count positions algorithm for large data unique positions, atoms: [25, 5, 25, 25, 76, 122, 122, 122, 122, 122, 122, 122, 122, 122, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 76, 122, 122, 122, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10] 244 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 283 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082405 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082405 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082405/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082405 Building REAL300000082406 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082406' /scratch/stefan/7930160/working/building/REAL300000082406 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082406 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082406/0 /scratch/stefan/7930160/working/building/REAL300000082406 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/433 `/scratch/stefan/7930160/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(CC)CC) `REAL300000082406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082406 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 69, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 46, 46, 46, 71, 71, 71, 71, 71, 46, 46, 46, 46, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 71 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082406 none CCOC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [8, 4, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 46, 70, 70, 46, 1, 1, 2, 1, 2, 8, 8, 8, 8, 8, 1, 1, 1, 1, 46, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 71 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 21, 28, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082406 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082406 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082406/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082406 Building REAL300000082407 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082407' /scratch/stefan/7930160/working/building/REAL300000082407 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082407 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082407/0 /scratch/stefan/7930160/working/building/REAL300000082407 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/434 `/scratch/stefan/7930160/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C) `REAL300000082407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082407 none COC1=CC=CC=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 126, 126, 126, 99, 126, 126, 66, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 80, 82, 148, 148, 148, 126, 126, 126, 126, 66, 66, 30, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300000082407 none COC1=CC=CC=C1CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 52, 52, 126, 126, 126, 126, 126, 126, 155, 155, 126, 15, 34, 34, 4, 4, 4, 1, 1, 1, 1, 7, 7, 15, 126, 126, 126, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082407 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082407 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082407/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082407 Building REAL300000082408 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082408' /scratch/stefan/7930160/working/building/REAL300000082408 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082408 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082408/0 /scratch/stefan/7930160/working/building/REAL300000082408 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/435 `/scratch/stefan/7930160/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC2=C(F)C=CC=C2C1=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082408 none CC1CCC2=C(F)C=CC=C2C1=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 4, 7, 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 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, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 1, 1, 1] 12 rigid atoms, others: [36, 37, 38, 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]) 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: REAL300000082408 none CC1CCC2=C(F)C=CC=C2C1=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 4, 7, 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 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, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34] set([35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 24 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082408 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082408 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082408/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082408 Building REAL300000082409 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082409' /scratch/stefan/7930160/working/building/REAL300000082409 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082409 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082409/0 /scratch/stefan/7930160/working/building/REAL300000082409 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/436 `/scratch/stefan/7930160/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082409 none CCN(C)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 8, 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, 6, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 132, 180, 66, 132, 132, 28, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 132, 132, 201, 201, 201, 201, 201, 180, 180, 180, 132, 132, 29, 29, 29, 6, 1, 1, 1, 132, 132] 201 rigid atoms, others: [38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 743 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082409 none CCN(C)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 8, 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, 6, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 1, 1, 13, 13, 13, 58, 132, 132, 132, 132, 132, 132, 188, 188, 132, 1, 1, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 13, 13, 13, 58, 132, 132, 132, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 41, 42, 22, 23] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 502 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082409 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082409 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082409/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082409 Building REAL300000082410 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082410' /scratch/stefan/7930160/working/building/REAL300000082410 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082410 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082410/0 /scratch/stefan/7930160/working/building/REAL300000082410 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/437 `/scratch/stefan/7930160/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1CN1C=CC=N1) `REAL300000082410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082410 none COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 78, 78, 78, 78, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 78, 78, 134, 201, 201, 201, 201, 92, 92, 92, 78, 78, 23, 23, 23, 5, 1, 1, 1, 78, 134, 134, 201, 201, 201] 201 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 552 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082410 none COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 37, 78, 78, 78, 78, 78, 78, 94, 94, 78, 1, 1, 1, 5, 21, 21, 21, 21, 4, 4, 4, 1, 1, 9, 9, 9, 37, 78, 78, 78, 1, 5, 5, 21, 21, 21] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 266 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082410 none COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 67, 67, 67, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 9, 1, 1, 1, 1, 1, 1, 33, 33, 33, 21, 21, 67, 67, 67, 168, 201, 201, 201, 21, 9, 9, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 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, 41, 42]) total number of confs: 542 number of broken/clashed sets: 88 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082410 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082410 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082410/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082410 Building REAL300000082411 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082411' /scratch/stefan/7930160/working/building/REAL300000082411 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082411 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082411/0 /scratch/stefan/7930160/working/building/REAL300000082411 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/438 `/scratch/stefan/7930160/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CN=C3)S2)=CC=C1F) `REAL300000082411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082411 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CN=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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: [140, 128, 140, 128, 128, 48, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 1, 128, 128, 128, 128, 128, 48, 8, 1, 5, 5, 5, 5, 128, 128] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082411 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CN=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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, 3, 1, 1, 1, 1, 13, 59, 59, 128, 128, 128, 128, 201, 201, 201, 201, 201, 128, 1, 1, 1, 1, 1, 13, 59, 128, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082411 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CN=C3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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, 201, 201, 115, 25, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 201, 201, 115, 25, 5, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082411 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082411 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082411/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082411 Building REAL300000082412 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082412' /scratch/stefan/7930160/working/building/REAL300000082412 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082412 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082412/0 /scratch/stefan/7930160/working/building/REAL300000082412 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/439 `/scratch/stefan/7930160/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC(F)F) `REAL300000082412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082412 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 84, 84, 84, 84, 84, 84, 119, 119, 84, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 9, 9, 9, 41, 84, 84, 84, 1, 1, 1, 33] 201 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 399 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082412 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 84, 84, 84, 84, 84, 84, 84, 165, 201, 201, 25, 25, 25, 4, 1, 1, 1, 84, 84, 84, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 470 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082412 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082412 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082412/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082412 Building REAL300000082413 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082413' /scratch/stefan/7930160/working/building/REAL300000082413 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082413 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082413/0 /scratch/stefan/7930160/working/building/REAL300000082413 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/440 `/scratch/stefan/7930160/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2CCCC3=CC=CC=C32)=CC=C1F) `REAL300000082413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082413 none O=C([O-])C1=CC(N=NCC2CCCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111] 111 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 38, 37]) total number of confs: 171 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: REAL300000082413 none O=C([O-])C1=CC(N=NCC2CCCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 9, 9, 59, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 59, 59, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1] 111 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 346 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082413 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082413 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082413/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082413 Building REAL300000082414 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082414' /scratch/stefan/7930160/working/building/REAL300000082414 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082414 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082414/0 /scratch/stefan/7930160/working/building/REAL300000082414 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/441 `/scratch/stefan/7930160/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC([N+](=O)[O-])=C3)C=C2)=CC=C1F) `REAL300000082414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082414 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC([N+](=O)[O-])=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 37, 25, 25, 12, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 15, 37, 37, 37, 37, 37, 1, 1, 25, 25, 25, 25, 25, 11, 3, 1, 1, 37, 37, 16, 37, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 38, 39, 8, 9, 10, 11, 12, 13, 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, 34, 35, 36, 37, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082414 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC([N+](=O)[O-])=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 25, 25, 17, 25, 101, 201, 201, 144, 201, 201, 201, 201, 201, 25, 25, 1, 1, 1, 1, 1, 5, 17, 25, 25, 201, 201, 152, 201, 25, 25, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 25, 26, 27, 28, 29] 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, 37, 38, 39]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082414 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC([N+](=O)[O-])=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 128, 66, 66, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 128, 66, 37, 37, 1, 1, 1, 1, 37, 37, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082414 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082414 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082414/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082414 Building REAL300000082415 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082415' /scratch/stefan/7930160/working/building/REAL300000082415 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082415 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082415/0 /scratch/stefan/7930160/working/building/REAL300000082415 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/442 `/scratch/stefan/7930160/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2CCOC3=CC=CC=C32)=CC=C1F) `REAL300000082415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082415 none O=C([O-])C1=CC(N=NCC2CCOC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 45, 45, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103] 103 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 36, 35]) total number of confs: 157 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: REAL300000082415 none O=C([O-])C1=CC(N=NCC2CCOC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 3, 1, 1, 1, 1, 9, 9, 55, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 55, 55, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1] 103 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 330 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082415 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082415 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082415/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082415 Building REAL300000082416 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082416' /scratch/stefan/7930160/working/building/REAL300000082416 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082416 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082416/0 /scratch/stefan/7930160/working/building/REAL300000082416 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/443 `/scratch/stefan/7930160/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1) `REAL300000082416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082416 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 62, 201, 62, 62, 62, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 201, 201, 201, 201, 201, 201, 62, 62, 33, 9, 1, 1, 1, 62] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 465 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082416 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 11, 13, 1, 11, 1, 1, 1, 1, 1, 6, 6, 31, 62, 62, 62, 62, 62, 62, 90, 90, 62, 1, 13, 13, 13, 13, 13, 13, 1, 1, 6, 31, 62, 62, 62, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 22, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 262 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082416 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082416 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082416/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082416 Building REAL300000082417 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082417' /scratch/stefan/7930160/working/building/REAL300000082417 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082417 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082417/0 /scratch/stefan/7930160/working/building/REAL300000082417 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/444 `/scratch/stefan/7930160/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082417 none COCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 195, 159, 72, 24, 24, 24, 16, 24, 24, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 195, 195, 159, 159, 24, 24, 24, 24, 16, 5, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082417 none COCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 73, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 24, 24, 24, 24, 24, 24, 35, 35, 24, 116, 116, 116, 73, 73, 35, 35, 1, 1, 1, 1, 4, 12, 24, 24, 24] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 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: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082417 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082417 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082417/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082417 Building REAL300000082418 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082418' /scratch/stefan/7930160/working/building/REAL300000082418 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082418 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082418/0 /scratch/stefan/7930160/working/building/REAL300000082418 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/445 `/scratch/stefan/7930160/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=NC2=CC=CC=C2S1) `REAL300000082418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082418 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=NC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 8, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 33, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 201, 201, 201, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082418 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=NC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 8, 1, 1, 1, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 97, 101, 201, 201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 39, 1, 1, 1, 101, 101, 101, 101, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 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: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082418 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082418 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082418/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082418 Building REAL300000082419 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082419' /scratch/stefan/7930160/working/building/REAL300000082419 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082419 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082419/0 /scratch/stefan/7930160/working/building/REAL300000082419 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/446 `/scratch/stefan/7930160/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C) `REAL300000082419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082419 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 13, 13, 34, 34, 34, 34, 34, 34, 46, 46, 34, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 10, 10, 10, 4, 4, 4, 4, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10] 57 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082419 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 34, 34, 34, 34, 34, 34, 45, 45, 57, 57, 57, 57, 24, 24, 24, 24, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 57, 57, 57, 57, 57, 57, 57, 57, 57] 57 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082419 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082419 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082419/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082419 Building REAL300000082420 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082420' /scratch/stefan/7930160/working/building/REAL300000082420 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082420 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082420/0 /scratch/stefan/7930160/working/building/REAL300000082420 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/447 `/scratch/stefan/7930160/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCC2)=CC=C1F) `REAL300000082420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082420 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 32, 30, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30] 33 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 55 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: REAL300000082420 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 30, 30, 30, 30, 30, 30, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082420 none O=C([O-])C1=CC(N=NC2CCCCC2[NH+]2CCCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 46, 47]) total number of confs: 49 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082420 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082420 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082420/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082420 Building REAL300000082421 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082421' /scratch/stefan/7930160/working/building/REAL300000082421 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082421 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082421/0 /scratch/stefan/7930160/working/building/REAL300000082421 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/448 `/scratch/stefan/7930160/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(CCCC2)S1) `REAL300000082421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082421 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 57, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 57, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1] 102 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082421 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [42, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 102, 102, 102, 102, 102, 102, 102, 102, 43, 43, 43, 11, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082421 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082421 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082421/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082421 Building REAL300000082422 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082422' /scratch/stefan/7930160/working/building/REAL300000082422 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082422 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082422/0 /scratch/stefan/7930160/working/building/REAL300000082422 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/449 `/scratch/stefan/7930160/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2)=C1) `REAL300000082422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082422 none COC1=CC=CC(CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 155, 155, 155, 155, 79, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 16, 28, 28, 16, 28, 28, 153, 201, 201, 201, 155, 155, 155, 79, 79, 5, 1, 1, 1, 28, 28, 16, 28, 28, 155] 201 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082422 none COC1=CC=CC(CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 28, 28, 83, 155, 155, 155, 155, 155, 155, 186, 186, 155, 28, 49, 49, 28, 49, 49, 1, 3, 3, 3, 1, 1, 1, 7, 7, 83, 155, 155, 155, 49, 49, 28, 49, 49, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 45, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082422 none COC1=CC=CC(CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 49, 49, 49, 49, 49, 22, 4, 1, 4, 4, 12, 28, 28, 28, 28, 28, 28, 38, 38, 28, 1, 1, 1, 1, 1, 1, 44, 79, 79, 79, 49, 49, 49, 22, 22, 12, 28, 28, 28, 1, 1, 1, 1, 1, 49] 201 rigid atoms, others: [8, 41, 42, 43, 44, 40, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 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, 45]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082422 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082422 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082422/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082422 Building REAL300000082423 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082423' /scratch/stefan/7930160/working/building/REAL300000082423 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082423 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082423/0 /scratch/stefan/7930160/working/building/REAL300000082423 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/450 `/scratch/stefan/7930160/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2F)CC2=CC=CC=C2F)=CC=C1F) `REAL300000082423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082423 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2F)CC2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 109, 134, 109, 109, 55, 55, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 42, 68, 68, 52, 68, 68, 68, 109, 109, 109, 109, 109, 17, 7, 7, 1, 1, 1, 1, 42, 42, 68, 68, 68, 68, 109, 109] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082423 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2F)CC2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 28, 67, 109, 109, 87, 109, 109, 109, 28, 66, 107, 107, 85, 107, 107, 107, 1, 1, 1, 1, 1, 28, 67, 67, 109, 109, 109, 109, 66, 66, 107, 107, 107, 107, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082423 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2F)CC2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 107, 130, 107, 107, 54, 54, 17, 7, 17, 40, 68, 68, 52, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 17, 40, 40, 68, 68, 68, 68, 7, 7, 1, 1, 1, 1, 107, 107] 201 rigid atoms, others: [39, 40, 41, 42, 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, 43, 44]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082423 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082423 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082423/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082423 Building REAL300000082424 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082424' /scratch/stefan/7930160/working/building/REAL300000082424 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082424 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082424/0 /scratch/stefan/7930160/working/building/REAL300000082424 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/451 `/scratch/stefan/7930160/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(Cl)S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082424 none CC(CCC1=CC=C(Cl)S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [37, 8, 37, 78, 105, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 37, 37, 85, 85, 99, 105, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082424 none CC(CCC1=CC=C(Cl)S1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 14, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [31, 11, 8, 1, 1, 1, 1, 1, 1, 1, 31, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 8, 8, 1, 1, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082424 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082424 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082424/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082424 Building REAL300000082425 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082425' /scratch/stefan/7930160/working/building/REAL300000082425 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082425 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082425/0 /scratch/stefan/7930160/working/building/REAL300000082425 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/452 `/scratch/stefan/7930160/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1Cl) `REAL300000082425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082425 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 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: [9, 1, 9, 9, 42, 111, 111, 111, 111, 111, 111, 152, 152, 111, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 9, 42, 111, 111, 111, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1] 179 rigid atoms, others: [1, 34, 35, 44, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 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: REAL300000082425 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 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: [30, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 111, 111, 31, 61, 179, 179, 179, 179, 179, 111, 111, 111, 31, 31, 31, 7, 1, 1, 1, 111, 111, 179, 179, 179, 179, 179, 179, 179, 179, 111] 179 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082425 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 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: [46, 10, 46, 46, 124, 179, 179, 179, 179, 179, 179, 179, 179, 179, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 46, 46, 46, 124, 179, 179, 179, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10] 179 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44]) total number of confs: 438 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082425 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082425 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082425/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082425 Building REAL300000082426 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082426' /scratch/stefan/7930160/working/building/REAL300000082426 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082426 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082426/0 /scratch/stefan/7930160/working/building/REAL300000082426 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/453 `/scratch/stefan/7930160/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N2C(C3CC3)=CSC2=N1) `REAL300000082426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082426 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N2C(C3CC3)=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 5, 5, 5, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 171, 171, 133, 133, 133, 133, 133, 133, 133, 35, 9, 1, 1, 1, 171, 171, 171, 171, 171, 133] 171 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 331 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082426 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N2C(C3CC3)=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 5, 5, 5, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 57, 133, 133, 133, 133, 133, 133, 157, 157, 133, 1, 1, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 11, 57, 133, 133, 133, 7, 7, 7, 7, 7, 1] 171 rigid atoms, others: [0, 1, 2, 3, 38, 16, 17, 18, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 355 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082426 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N2C(C3CC3)=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 5, 5, 5, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 33, 33, 97, 171, 171, 171, 171, 171, 171, 171, 171, 171, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 30, 97, 171, 171, 171, 1, 1, 1, 1, 1, 7] 171 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 343 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082426 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082426 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082426/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082426 Building REAL300000082427 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082427' /scratch/stefan/7930160/working/building/REAL300000082427 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082427 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082427/0 /scratch/stefan/7930160/working/building/REAL300000082427 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/454 `/scratch/stefan/7930160/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1) `REAL300000082427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none CN1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 33, 57, 57, 57, 57, 57, 57, 72, 72, 57, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 5, 33, 57, 57, 57, 1, 11, 11, 11, 11] 94 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 39, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none CN1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 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, 11, 11, 1, 2, 35, 35, 79, 94, 94, 94, 94, 94, 94, 94, 94, 94, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 11, 34, 79, 94, 94, 94, 11, 1, 1, 1, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 41, 42, 43, 24, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none CN1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 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, 46, 43, 57, 57, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 57, 94, 94, 94, 94, 94, 94, 94, 94, 94, 57, 30, 6, 1, 1, 1, 57, 94, 94, 94, 94] 94 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082427 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082427/1 /scratch/stefan/7930160/working/building/REAL300000082427 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/455 `/scratch/stefan/7930160/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1) `REAL300000082427.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none C[NH+]1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 6, 6, 39, 69, 69, 68, 68, 69, 69, 82, 82, 69, 1, 1, 12, 12, 13, 13, 13, 12, 12, 12, 12, 1, 6, 39, 69, 69, 69, 1, 12, 12, 12, 12] 99 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 40, 23, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none C[NH+]1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 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, 12, 12, 1, 12, 43, 43, 88, 99, 99, 99, 99, 99, 99, 99, 99, 99, 12, 12, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 43, 88, 99, 99, 99, 12, 1, 1, 1, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 41, 42, 43, 44, 33, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082427 none C[NH+]1CCN(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=N2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 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, 69, 69, 69, 69, 34, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 99, 99, 99, 99, 99, 99, 99, 99, 99, 69, 34, 6, 1, 1, 1, 69, 99, 99, 99, 99] 99 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 157 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082427 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082427 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082427/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082427/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082427 Building REAL300000082428 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082428' /scratch/stefan/7930160/working/building/REAL300000082428 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082428 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082428/0 /scratch/stefan/7930160/working/building/REAL300000082428 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/456 `/scratch/stefan/7930160/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(C(F)(F)F)C=C32)=CC=C1F) `REAL300000082428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082428 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(C(F)(F)F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 26, 26, 27, 7, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 33, 22, 23, 24, 25, 26, 27]) 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: REAL300000082428 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(C(F)(F)F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082428 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082428 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082428/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082428 Building REAL300000082429 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082429' /scratch/stefan/7930160/working/building/REAL300000082429 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082429 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082429/0 /scratch/stefan/7930160/working/building/REAL300000082429 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/457 `/scratch/stefan/7930160/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=CC(OC)=C2O1) `REAL300000082429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082429 none COC(=O)C1=CC2=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=CC(OC)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 10, 23, 10, 10, 10, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 10, 10, 10, 10, 17, 10, 10, 23, 23, 23, 10, 6, 4, 1, 1, 1, 10, 10, 17, 17, 17] 25 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) 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: REAL300000082429 none COC(=O)C1=CC2=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=CC(OC)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 10, 10, 16, 16, 10, 1, 1, 1, 1, 3, 1, 1, 9, 9, 9, 1, 3, 5, 10, 10, 10, 1, 1, 3, 3, 3] 25 rigid atoms, others: [2, 4, 5, 6, 7, 8, 38, 21, 22, 23, 24, 26, 27, 37, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082429 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082429 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082429/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082429 Building REAL300000082430 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082430' /scratch/stefan/7930160/working/building/REAL300000082430 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082430 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082430/0 /scratch/stefan/7930160/working/building/REAL300000082430 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/458 `/scratch/stefan/7930160/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C2C=CC(=O)N3)=CC=C1F) `REAL300000082430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082430 none O=C([O-])C1=CC(NN=C2CCCC3=C2C=CC(=O)N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 61 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082430 none O=C([O-])C1=CC(NN=C2CCCC3=C2C=CC(=O)N3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1] 42 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082430 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082430 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082430/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082430 Building REAL300000082431 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082431' /scratch/stefan/7930160/working/building/REAL300000082431 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082431 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082431/0 /scratch/stefan/7930160/working/building/REAL300000082431 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/459 `/scratch/stefan/7930160/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(CC2=CC=CC=C2)N=C1) `REAL300000082431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082431 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 64, 64, 64, 64, 64, 64, 89, 89, 64, 1, 1, 1, 1, 8, 14, 14, 11, 14, 14, 1, 1, 7, 7, 7, 32, 64, 64, 64, 1, 8, 8, 14, 14, 14, 14, 14, 1] 201 rigid atoms, others: [1, 33, 41, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000082431 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 19, 64, 64, 64, 151, 201, 201, 176, 201, 201, 64, 64, 19, 19, 19, 5, 1, 1, 1, 64, 151, 151, 201, 201, 201, 201, 201, 64] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 694 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082431 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 68, 68, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 68, 68, 68, 140, 201, 201, 201, 14, 4, 4, 1, 1, 1, 1, 1, 14] 201 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: 476 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082431 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082431 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082431/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082431 Building REAL300000082432 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082432' /scratch/stefan/7930160/working/building/REAL300000082432 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082432 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082432/0 /scratch/stefan/7930160/working/building/REAL300000082432 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/460 `/scratch/stefan/7930160/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082432 none N#CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 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, 68, 68, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 144, 144, 144, 144, 144, 144, 68, 13, 1, 1, 1, 144] 144 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) 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: REAL300000082432 none N#CC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 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, 8, 8, 56, 144, 144, 144, 144, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 8, 55, 144, 144, 144, 1] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082432 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082432 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082432/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082432 Building REAL300000082433 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082433' /scratch/stefan/7930160/working/building/REAL300000082433 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082433 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082433/0 /scratch/stefan/7930160/working/building/REAL300000082433 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/461 `/scratch/stefan/7930160/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(N3C=CC=N3)=C2)=CC=C1F) `REAL300000082433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082433 none O=C([O-])C1=CC(NN=CC2=CC=CC(N3C=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 39, 39, 38, 38, 39, 22, 6, 1, 1, 1, 5, 5, 5, 1, 39, 39] 44 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 35]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082433 none O=C([O-])C1=CC(NN=CC2=CC=CC(N3C=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 7, 25, 25, 39, 39, 39, 39, 39, 44, 44, 44, 44, 39, 1, 1, 1, 1, 1, 7, 25, 39, 39, 39, 44, 44, 44, 39, 1, 1] 44 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082433 none O=C([O-])C1=CC(NN=CC2=CC=CC(N3C=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 12, 12, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 44, 44, 44, 44, 44, 36, 12, 4, 5, 5, 1, 1, 1, 5, 44, 44] 44 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082433 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082433 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082433/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082433 Building REAL300000082434 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082434' /scratch/stefan/7930160/working/building/REAL300000082434 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082434 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082434/0 /scratch/stefan/7930160/working/building/REAL300000082434 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/462 `/scratch/stefan/7930160/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3CCC3)S2)=CC=C1F) `REAL300000082434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082434 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 83, 124, 83, 83, 39, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 1, 83, 83, 82, 82, 83, 39, 6, 1, 13, 13, 13, 13, 13, 13, 13, 83, 83] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082434 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 42, 42, 83, 83, 83, 83, 201, 201, 201, 83, 1, 1, 1, 1, 1, 10, 42, 83, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082434 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 52, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 142, 52, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082434 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082434 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082434/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082434 Building REAL300000082435 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082435' /scratch/stefan/7930160/working/building/REAL300000082435 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082435 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082435/0 /scratch/stefan/7930160/working/building/REAL300000082435 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/463 `/scratch/stefan/7930160/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN=C1Cl) `REAL300000082435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082435 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 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, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 111, 111, 111, 111, 111, 111, 111, 111, 51, 13, 1, 1, 1, 111] 111 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) 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: REAL300000082435 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 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, 9, 9, 58, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 2, 2, 2, 1, 9, 58, 111, 111, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082435 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082435 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082435/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082435 Building REAL300000082436 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082436' /scratch/stefan/7930160/working/building/REAL300000082436 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082436 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082436/0 /scratch/stefan/7930160/working/building/REAL300000082436 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/464 `/scratch/stefan/7930160/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=C(F)C=C2O1) `REAL300000082436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082436 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=C(F)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 10, 1, 1, 1, 39, 39, 39] 39 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 66 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: REAL300000082436 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=C(F)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 39, 39, 39, 1, 1, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 39, 17, 18, 19, 20, 21, 22, 23, 24, 38, 37, 31] set([33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082436 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082436 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082436/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082436 Building REAL300000082437 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082437' /scratch/stefan/7930160/working/building/REAL300000082437 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082437 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082437/0 /scratch/stefan/7930160/working/building/REAL300000082437 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/465 `/scratch/stefan/7930160/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082437 none CC(C)(C)OC(=O)N1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 168, 106, 168, 106, 106, 97, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 36, 36, 1, 1, 1, 106, 106, 106, 106] 201 rigid atoms, others: [42, 43, 44, 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, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082437 none CC(C)(C)OC(=O)N1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 8, 53, 53, 106, 106, 106, 106, 106, 106, 150, 150, 106, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 1, 1, 1, 1, 8, 8, 106, 106, 106, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 45, 46, 47, 48, 24, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082437 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082437 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082437/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082437 Building REAL300000082438 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082438' /scratch/stefan/7930160/working/building/REAL300000082438 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082438 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082438/0 /scratch/stefan/7930160/working/building/REAL300000082438 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/466 `/scratch/stefan/7930160/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)OC1=CC=C(Cl)C=C1Cl) `REAL300000082438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082438 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)OC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 13, 33, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 201, 201, 201, 13, 13, 13, 13, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 383 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: REAL300000082438 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)OC1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 95, 97, 173, 201, 201, 188, 201, 201, 201, 201, 37, 37, 37, 37, 1, 1, 1, 97, 97, 97, 97, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 609 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082438 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082438 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082438/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082438 Building REAL300000082439 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082439' /scratch/stefan/7930160/working/building/REAL300000082439 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082439 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082439/0 /scratch/stefan/7930160/working/building/REAL300000082439 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/467 `/scratch/stefan/7930160/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(Br)C(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082439 none CC(CC1=CC=C(Br)C(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 17, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 50, 113, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 50, 50, 50, 113, 113, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082439 none CC(CC1=CC=C(Br)C(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 17, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 14, 87, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 14, 6, 6, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082439 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082439 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082439/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082439 Building REAL300000082440 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082440' /scratch/stefan/7930160/working/building/REAL300000082440 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082440 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082440/0 /scratch/stefan/7930160/working/building/REAL300000082440 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/468 `/scratch/stefan/7930160/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C2SC2=CC=CC=C23)=CC=C1F) `REAL300000082440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082440 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 38, 21, 22, 23, 24, 25, 26, 37]) 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: REAL300000082440 none O=C([O-])C1=CC(NN=C2CCCC3=C2SC2=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082440 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082440 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082440/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082440 Building REAL300000082441 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082441' /scratch/stefan/7930160/working/building/REAL300000082441 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082441 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082441/0 /scratch/stefan/7930160/working/building/REAL300000082441 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/469 `/scratch/stefan/7930160/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=N1) `REAL300000082441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082441 none CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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, 111, 86, 86, 86, 86, 86, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 139, 139, 139, 139, 139, 86, 86, 86, 51, 11, 1, 1, 1] 139 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082441 none CCOC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [16, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 86, 86, 85, 85, 86, 86, 118, 118, 86, 1, 16, 16, 16, 16, 16, 1, 1, 1, 6, 30, 86, 86, 86] 139 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082441 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082441 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082441/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082441 Building REAL300000082442 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082442' /scratch/stefan/7930160/working/building/REAL300000082442 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082442 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082442/0 /scratch/stefan/7930160/working/building/REAL300000082442 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/470 `/scratch/stefan/7930160/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1) `REAL300000082442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082442 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 1, 9, 9, 40, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 88, 88, 88, 1, 1, 1] 88 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 167 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082442 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 86, 86, 86, 86, 86, 86, 86, 45, 45, 45, 11, 1, 1, 1, 86, 86, 86] 86 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082442 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082442 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082442/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082442 Building REAL300000082443 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082443' /scratch/stefan/7930160/working/building/REAL300000082443 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082443 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082443/0 /scratch/stefan/7930160/working/building/REAL300000082443 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/471 `/scratch/stefan/7930160/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=CC=C1F) `REAL300000082443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082443 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 87, 126, 87, 87, 30, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 22, 1, 1, 87, 87, 87, 87, 87, 29, 4, 1, 1, 10, 10, 22, 22, 22, 22, 1, 1, 87, 87] 201 rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 40, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 391 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: REAL300000082443 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 53, 53, 87, 87, 55, 87, 138, 159, 201, 201, 159, 201, 201, 201, 87, 87, 1, 1, 1, 1, 1, 11, 53, 87, 87, 159, 159, 201, 201, 201, 201, 87, 87, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 786 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082443 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 130, 37, 37, 22, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 201, 129, 37, 22, 22, 3, 3, 1, 1, 1, 1, 22, 22, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 429 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082443 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082443 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082443/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082443 Building REAL300000082444 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082444' /scratch/stefan/7930160/working/building/REAL300000082444 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082444 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082444/0 /scratch/stefan/7930160/working/building/REAL300000082444 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/472 `/scratch/stefan/7930160/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082444 none CSC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 89, 89, 89, 56, 89, 89, 89, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 125, 125, 125, 89, 89, 89, 45, 11, 1, 1, 1] 125 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082444 none CSC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 89, 89, 89, 89, 89, 89, 99, 99, 89, 9, 9, 9, 1, 1, 1, 8, 34, 89, 89, 89] 125 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 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/7930160/working/building/REAL300000082444 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082444 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082444/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082444 Building REAL300000082445 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082445' /scratch/stefan/7930160/working/building/REAL300000082445 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082445 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082445/0 /scratch/stefan/7930160/working/building/REAL300000082445 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/473 `/scratch/stefan/7930160/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082445 none CC1=C(Br)SC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 17, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 45, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 79, 79, 45, 13, 1, 1, 1, 79] 79 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 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: REAL300000082445 none CC1=C(Br)SC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 17, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 79, 79, 79, 79, 79, 79, 79, 79, 79, 1, 2, 2, 2, 8, 46, 79, 79, 79, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082445 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082445 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082445/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082445 Building REAL300000082446 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082446' /scratch/stefan/7930160/working/building/REAL300000082446 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082446 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082446/0 /scratch/stefan/7930160/working/building/REAL300000082446 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/474 `/scratch/stefan/7930160/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1Br) `REAL300000082446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082446 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 91, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 91, 91, 91, 1, 1, 1] 91 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 169 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082446 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 91, 91, 76, 76, 91, 91, 91, 52, 52, 52, 11, 1, 1, 1, 91, 91, 91] 91 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082446 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082446 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082446/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082446 Building REAL300000082447 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082447' /scratch/stefan/7930160/working/building/REAL300000082447 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082447 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082447/0 /scratch/stefan/7930160/working/building/REAL300000082447 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/475 `/scratch/stefan/7930160/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(F)=C2)=CC=C1F) `REAL300000082447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082447 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 114, 113, 113, 114, 55, 8, 1, 1, 1, 114, 114] 114 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082447 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 51, 51, 114, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 13, 51, 114, 114, 114, 1, 1] 114 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082447 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082447 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082447/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082447 Building REAL300000082448 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082448' /scratch/stefan/7930160/working/building/REAL300000082448 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082448 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082448/0 /scratch/stefan/7930160/working/building/REAL300000082448 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/476 `/scratch/stefan/7930160/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(CC(F)(F)F)N=C2)=CC=C1F) `REAL300000082448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082448 none O=C([O-])C1=CC(NN=CC2=CN(CC(F)(F)F)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 89, 111, 89, 89, 39, 7, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 89, 89, 89, 89, 89, 39, 7, 1, 9, 9, 1, 89, 89] 201 rigid atoms, others: [8, 9, 10, 11, 12, 17, 18, 26, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 31]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082448 none O=C([O-])C1=CC(NN=CC2=CN(CC(F)(F)F)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 41, 41, 89, 89, 89, 201, 201, 201, 201, 89, 89, 1, 1, 1, 1, 1, 9, 41, 88, 201, 201, 89, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082448 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082448 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082448/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082448 Building REAL300000082449 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082449' /scratch/stefan/7930160/working/building/REAL300000082449 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082449 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082449/0 /scratch/stefan/7930160/working/building/REAL300000082449 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/477 `/scratch/stefan/7930160/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC)C=C1O) `REAL300000082449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082449 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [181, 122, 122, 122, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 122, 122, 146, 122, 122, 122, 181, 181, 181, 122, 32, 32, 32, 6, 1, 1, 1, 146, 146, 146, 122, 244] 402 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 575 number of broken/clashed sets: 176 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082449 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(OC)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 13, 44, 122, 122, 122, 122, 122, 122, 184, 184, 122, 1, 1, 4, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 44, 122, 122, 122, 4, 4, 4, 1, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 39, 19, 20, 22, 23, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 486 number of broken/clashed sets: 176 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082449 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082449 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082449/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082449 Building REAL300000082450 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082450' /scratch/stefan/7930160/working/building/REAL300000082450 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082450 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082450/0 /scratch/stefan/7930160/working/building/REAL300000082450 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/478 `/scratch/stefan/7930160/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1F) `REAL300000082450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082450 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 133, 133, 133, 1, 1, 1] 133 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082450 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 133, 133, 133, 133, 133, 133, 133, 47, 47, 47, 10, 1, 1, 1, 133, 133, 133] 133 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082450 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082450 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082450/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082450 Building REAL300000082451 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082451' /scratch/stefan/7930160/working/building/REAL300000082451 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082451 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082451/0 /scratch/stefan/7930160/working/building/REAL300000082451 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/479 `/scratch/stefan/7930160/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(CCS(C)(=O)=O)N=C1C) `REAL300000082451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082451 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(CCS(C)(=O)=O)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 14, 5, 11, 11, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 69, 69, 69, 69, 69, 69, 96, 96, 69, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 1, 1, 1, 7, 7, 7, 30, 69, 69, 69, 2, 2, 2, 5, 5, 5, 5, 26, 26, 26, 2, 2, 2] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300000082451 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(CCS(C)(=O)=O)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 14, 5, 11, 11, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 69, 69, 69, 69, 165, 165, 201, 201, 201, 69, 69, 69, 25, 25, 25, 5, 1, 1, 1, 69, 69, 69, 165, 165, 165, 165, 201, 201, 201, 69, 69, 69] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 725 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082451 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082451 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082451/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082451 Building REAL300000082452 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082452' /scratch/stefan/7930160/working/building/REAL300000082452 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082452 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082452/0 /scratch/stefan/7930160/working/building/REAL300000082452 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/480 `/scratch/stefan/7930160/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082452 none CC1=CC=C2C(=C1)OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1] 33 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082452 none CC1=CC=C2C(=C1)OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 32, 33, 33, 32, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082452 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082452 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082452/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082452 Building REAL300000082453 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082453' /scratch/stefan/7930160/working/building/REAL300000082453 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082453 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082453/0 /scratch/stefan/7930160/working/building/REAL300000082453 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/481 `/scratch/stefan/7930160/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082453 none CC1=CC(C)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 35, 35, 35, 34, 35, 35, 35, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 34] 35 rigid atoms, others: [39, 40, 41, 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, 35, 36, 37, 38, 42]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082453 none CC1=CC(C)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 34, 34, 34, 35, 35, 34, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 28, 32, 33, 34, 35, 36, 37, 42] set([38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082453 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082453 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082453/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082453 Building REAL300000082454 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082454' /scratch/stefan/7930160/working/building/REAL300000082454 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082454 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082454/0 /scratch/stefan/7930160/working/building/REAL300000082454 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/482 `/scratch/stefan/7930160/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CSCCC3=CC=CC=C32)=CC=C1F) `REAL300000082454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082454 none O=C([O-])C1=CC(NN=C2CSCCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 23, 24, 36]) total number of confs: 46 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: REAL300000082454 none O=C([O-])C1=CC(NN=C2CSCCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082454 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082454 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082454/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082454 Building REAL300000082455 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082455' /scratch/stefan/7930160/working/building/REAL300000082455 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082455 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082455/0 /scratch/stefan/7930160/working/building/REAL300000082455 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/483 `/scratch/stefan/7930160/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=CC=CN=C23)=CC=C1F) `REAL300000082455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082455 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 26, 6, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082455 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 45, 45, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 11, 45, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082455 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082455 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082455/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082455 Building REAL300000082456 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082456' /scratch/stefan/7930160/working/building/REAL300000082456 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082456 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082456/0 /scratch/stefan/7930160/working/building/REAL300000082456 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/484 `/scratch/stefan/7930160/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C3COCC3=C2)=CC=C1F) `REAL300000082456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082456 none O=C([O-])C1=CC(NN=CC2=CC=C3COCC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 53, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 118, 118, 119, 53, 9, 1, 1, 1, 1, 1, 1, 1, 119, 119] 119 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082456 none O=C([O-])C1=CC(NN=CC2=CC=C3COCC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 53, 53, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 13, 53, 119, 119, 119, 119, 119, 119, 119, 1, 1] 119 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082456 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082456 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082456/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082456 Building REAL300000082457 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082457' /scratch/stefan/7930160/working/building/REAL300000082457 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082457 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082457/0 /scratch/stefan/7930160/working/building/REAL300000082457 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/485 `/scratch/stefan/7930160/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082457 none COC1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 38, 58, 58, 58, 38, 38, 38, 38, 38, 38, 38, 38, 11, 1, 1, 1, 38] 58 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40]) 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: REAL300000082457 none COC1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 38, 38, 37, 37, 38, 38, 58, 58, 38, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 38, 38, 38, 1] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 40] set([0, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082457 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082457 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082457/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082457 Building REAL300000082458 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082458' /scratch/stefan/7930160/working/building/REAL300000082458 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082458 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082458/0 /scratch/stefan/7930160/working/building/REAL300000082458 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/486 `/scratch/stefan/7930160/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082458 none CC(C)CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 71, 81, 67, 52, 67, 67, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 67, 81, 81, 81, 81, 81, 81, 81, 71, 71, 67, 67, 28, 9, 1, 1, 1, 67, 67] 81 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082458 none CC(C)CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 1, 1, 1, 1, 1, 1, 6, 6, 28, 67, 67, 67, 67, 67, 67, 77, 77, 67, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 6, 28, 67, 67, 67, 1, 1] 81 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 39, 40, 21, 22] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082458 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082458 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082458/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082458 Building REAL300000082459 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082459' /scratch/stefan/7930160/working/building/REAL300000082459 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082459 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082459/0 /scratch/stefan/7930160/working/building/REAL300000082459 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/487 `/scratch/stefan/7930160/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=N3)=C2)=CC=C1F) `REAL300000082459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082459 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [92, 76, 92, 76, 76, 28, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 76, 76, 75, 75, 76, 28, 4, 1, 11, 11, 11, 11, 1, 76, 76] 113 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34]) 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: REAL300000082459 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 54, 54, 76, 76, 76, 76, 113, 113, 113, 113, 113, 76, 1, 1, 1, 1, 1, 11, 54, 76, 113, 113, 113, 113, 76, 1, 1] 113 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082459 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 82, 25, 25, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 113, 113, 112, 112, 113, 83, 26, 11, 1, 1, 1, 1, 11, 113, 113] 113 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 262 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082459 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082459 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082459/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082459 Building REAL300000082460 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082460' /scratch/stefan/7930160/working/building/REAL300000082460 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082460 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082460/0 /scratch/stefan/7930160/working/building/REAL300000082460 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/488 `/scratch/stefan/7930160/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082460 none CCC1=NOC(C)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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, 143, 143, 143, 143, 143, 143, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 143, 143, 143, 33, 33, 33, 6, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 531 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082460 none CCC1=NOC(C)=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 143, 143, 143, 143, 143, 143, 171, 171, 143, 8, 8, 8, 7, 7, 2, 2, 2, 10, 10, 10, 52, 143, 143, 143] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 400 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082460 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082460 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082460/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082460 Building REAL300000082461 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082461' /scratch/stefan/7930160/working/building/REAL300000082461 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082461 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082461/0 /scratch/stefan/7930160/working/building/REAL300000082461 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/489 `/scratch/stefan/7930160/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082461 none CC(C)C1=CC=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 36, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 38, 38, 38, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1] 38 rigid atoms, others: [43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082461 none CC(C)C1=CC=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36, 36, 36, 36, 38, 38, 36, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36] 38 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082461 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082461 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082461/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082461 Building REAL300000082462 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082462' /scratch/stefan/7930160/working/building/REAL300000082462 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082462 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082462/0 /scratch/stefan/7930160/working/building/REAL300000082462 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/490 `/scratch/stefan/7930160/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=CC4=C(C=C32)CCC4)=CC=C1F) `REAL300000082462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082462 none O=C([O-])C1=CC(NN=C2CCCOC3=CC4=C(C=C32)CCC4)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 42, 43, 22, 23, 24, 25, 26, 27]) 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: REAL300000082462 none O=C([O-])C1=CC(NN=C2CCCOC3=CC4=C(C=C32)CCC4)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082462 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082462 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082462/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082462 Building REAL300000082463 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082463' /scratch/stefan/7930160/working/building/REAL300000082463 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082463 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082463/0 /scratch/stefan/7930160/working/building/REAL300000082463 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/491 `/scratch/stefan/7930160/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082463 none CC1=CC(Cl)=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 37, 36, 36, 36, 36, 36, 36, 36, 36, 9, 1, 1, 1] 37 rigid atoms, others: [37, 38, 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, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082463 none CC1=CC(Cl)=CC2=C1OCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36, 36, 36, 36, 37, 37, 36, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35] set([36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082463 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082463 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082463/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082463 Building REAL300000082464 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082464' /scratch/stefan/7930160/working/building/REAL300000082464 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082464 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082464/0 /scratch/stefan/7930160/working/building/REAL300000082464 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/492 `/scratch/stefan/7930160/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082464 none COC1=CC=CC2=C1CCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 80, 80, 80, 55, 55, 55, 55, 55, 55, 55, 10, 1, 1, 1] 80 rigid atoms, others: [34, 35, 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, 33]) 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: REAL300000082464 none COC1=CC=CC2=C1CCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 55, 55, 55, 55, 80, 80, 55, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 55] 80 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082464 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082464 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082464/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082464 Building REAL300000082465 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082465' /scratch/stefan/7930160/working/building/REAL300000082465 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082465 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082465/0 /scratch/stefan/7930160/working/building/REAL300000082465 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/493 `/scratch/stefan/7930160/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2Br)=CC=C1F) `REAL300000082465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082465 none O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 48, 9, 1, 2, 1, 1, 75, 75] 150 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 25, 28, 29]) 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: REAL300000082465 none O=C([O-])C1=CC(NN=CC2=CC(O)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 10, 41, 41, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 10, 41, 75, 150, 75, 75, 1, 1] 150 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082465 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082465 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082465/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082465 Building REAL300000082466 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082466' /scratch/stefan/7930160/working/building/REAL300000082466 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082466 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082466/0 /scratch/stefan/7930160/working/building/REAL300000082466 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/494 `/scratch/stefan/7930160/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082466 none CC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 69, 85, 85, 85, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 85, 85, 85, 85, 85, 85, 53, 13, 1, 1, 1] 85 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: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082466 none CC1=CC(Br)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 10, 10, 46, 85, 85, 85, 85, 85, 85, 85, 85, 85, 2, 2, 2, 1, 1, 1, 10, 46, 85, 85, 85] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082466 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082466 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082466/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082466 Building REAL300000082467 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082467' /scratch/stefan/7930160/working/building/REAL300000082467 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082467 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082467/0 /scratch/stefan/7930160/working/building/REAL300000082467 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/495 `/scratch/stefan/7930160/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082467 none CCSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 156, 94, 94, 94, 65, 94, 94, 38, 38, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 94, 94, 94, 94, 38, 38, 38, 9, 1, 1, 1] 201 rigid atoms, others: [36, 37, 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, 35]) total number of confs: 660 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082467 none CCSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 94, 94, 94, 94, 94, 94, 148, 148, 94, 32, 31, 31, 31, 31, 1, 1, 1, 1, 7, 7, 7, 31, 94, 94, 94] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 474 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082467 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082467 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082467/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082467 Building REAL300000082468 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082468' /scratch/stefan/7930160/working/building/REAL300000082468 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082468 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082468/0 /scratch/stefan/7930160/working/building/REAL300000082468 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/496 `/scratch/stefan/7930160/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2)C=C1) `REAL300000082468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082468 none CC1=CC=C(C2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 141, 141, 140, 140, 141, 141, 201, 201, 141, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 11, 58, 141, 141, 141, 1, 3, 3] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 39, 23, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 40, 41]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082468 none CC1=CC=C(C2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 31, 115, 201, 201, 201, 5, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082468 none CC1=CC=C(C2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 141, 141, 141, 141, 141, 54, 54, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 141, 201, 201, 201, 201, 201, 201, 201, 141, 141, 141, 54, 9, 1, 1, 1, 141, 201, 201] 201 rigid atoms, others: [36, 37, 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, 35, 39, 40, 41]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082468 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082468 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082468/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082468 Building REAL300000082469 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082469' /scratch/stefan/7930160/working/building/REAL300000082469 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082469 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082469/0 /scratch/stefan/7930160/working/building/REAL300000082469 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/497 `/scratch/stefan/7930160/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C21) `REAL300000082469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082469 none CC(C)(C)OC(=O)N1CCC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 181, 183, 183, 107, 101, 107, 101, 101, 101, 101, 101, 101, 101, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 183, 183, 183, 183, 183, 183, 183, 183, 183, 101, 101, 101, 101, 101, 101, 101, 52, 11, 1, 1, 1] 183 rigid atoms, others: [49, 47, 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, 45, 46]) total number of confs: 315 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: REAL300000082469 none CC(C)(C)OC(=O)N1CCC2=CC=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [15, 12, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 101, 101, 101, 101, 101, 101, 140, 140, 101, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 5, 26, 101, 101, 101] 183 rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 15, 28, 42] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49]) total number of confs: 350 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082469 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082469 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082469/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082469 Building REAL300000082470 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082470' /scratch/stefan/7930160/working/building/REAL300000082470 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082470 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082470/0 /scratch/stefan/7930160/working/building/REAL300000082470 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/498 `/scratch/stefan/7930160/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CN=C3)=C2)=CC=C1F) `REAL300000082470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082470 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 85, 120, 85, 85, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 85, 85, 84, 84, 85, 44, 7, 1, 1, 1, 5, 5, 5, 5, 1, 85, 85] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36, 37]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082470 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 33, 33, 85, 85, 85, 85, 85, 201, 201, 201, 201, 201, 85, 1, 1, 1, 1, 1, 9, 33, 85, 85, 85, 201, 201, 201, 201, 85, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082470 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 124, 26, 26, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 201, 201, 124, 26, 5, 5, 5, 1, 1, 1, 1, 5, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 412 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082470 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082470 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082470/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082470 Building REAL300000082471 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082471' /scratch/stefan/7930160/working/building/REAL300000082471 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082471 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082471/0 /scratch/stefan/7930160/working/building/REAL300000082471 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/499 `/scratch/stefan/7930160/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2Br)=CC=C1F) `REAL300000082471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082471 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 39, 10, 1, 1, 1, 76, 76] 76 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082471 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 43, 43, 76, 76, 43, 56, 76, 76, 76, 1, 1, 1, 1, 1, 11, 43, 76, 76, 76, 1, 1] 76 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082471 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082471 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082471/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082471 Building REAL300000082472 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082472' /scratch/stefan/7930160/working/building/REAL300000082472 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082472 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082472/0 /scratch/stefan/7930160/working/building/REAL300000082472 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/500 `/scratch/stefan/7930160/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[NH+](CC2=CC=CC=C2)CC(C)C1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082472 none CC1C[NH+](CC2=CC=CC=C2)CC(C)C1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 9, 3, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 73, 73, 73, 73, 73, 73, 73, 73, 73, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 73, 73, 73] 73 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 126 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: REAL300000082472 none CC1C[NH+](CC2=CC=CC=C2)CC(C)C1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 27, 33, 33, 27, 2, 2, 2, 1, 1, 1, 8, 8, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27] 73 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 41, 42, 43, 12, 13, 14, 15, 16, 47, 5, 31] set([6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082472 none CC1C[NH+](CC2=CC=CC=C2)CC(C)C1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 67, 73, 73, 73, 73, 73, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 27, 67, 67, 73, 73, 73, 73, 73, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1] 73 rigid atoms, others: [49, 50, 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, 45, 46, 47]) total number of confs: 272 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082472 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082472 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082472/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082472 Building REAL300000082473 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082473' /scratch/stefan/7930160/working/building/REAL300000082473 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082473 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082473/0 /scratch/stefan/7930160/working/building/REAL300000082473 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/501 `/scratch/stefan/7930160/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3CC3)S2)=CC=C1F) `REAL300000082473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082473 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 129, 93, 93, 39, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 1, 93, 93, 93, 93, 93, 39, 6, 1, 12, 12, 12, 12, 12, 93, 93] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082473 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 46, 46, 93, 93, 93, 93, 201, 201, 93, 1, 1, 1, 1, 1, 10, 46, 93, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082473 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 154, 48, 48, 12, 12, 12, 12, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 154, 48, 12, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082473 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082473 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082473/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082473 Building REAL300000082474 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082474' /scratch/stefan/7930160/working/building/REAL300000082474 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082474 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082474/0 /scratch/stefan/7930160/working/building/REAL300000082474 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/502 `/scratch/stefan/7930160/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082474 none CC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [56, 8, 56, 121, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 56, 121, 121, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082474 none CC(CC1=CC=CC(F)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082474 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082474 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082474/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082474 Building REAL300000082475 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082475' /scratch/stefan/7930160/working/building/REAL300000082475 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082475 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082475/0 /scratch/stefan/7930160/working/building/REAL300000082475 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/503 `/scratch/stefan/7930160/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCC3)S2)=CC=C1F) `REAL300000082475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082475 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 118, 86, 86, 40, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 86, 86, 85, 85, 86, 40, 8, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 86, 86] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082475 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 41, 41, 86, 86, 86, 86, 201, 201, 201, 201, 86, 1, 1, 1, 1, 1, 10, 41, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082475 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 141, 47, 46, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 141, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082475 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082475 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082475/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082475 Building REAL300000082476 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082476' /scratch/stefan/7930160/working/building/REAL300000082476 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082476 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082476/0 /scratch/stefan/7930160/working/building/REAL300000082476 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/504 `/scratch/stefan/7930160/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2F)=CC=C1F) `REAL300000082476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082476 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 35, 7, 1, 1, 1, 59, 59] 59 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082476 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 39, 39, 59, 59, 58, 59, 59, 59, 59, 1, 1, 1, 1, 1, 10, 39, 59, 59, 58, 1, 1] 59 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082476 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082476 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082476/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082476 Building REAL300000082477 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082477' /scratch/stefan/7930160/working/building/REAL300000082477 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082477 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082477/0 /scratch/stefan/7930160/working/building/REAL300000082477 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/505 `/scratch/stefan/7930160/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1) `REAL300000082477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082477 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 7, 1, 7, 7, 41, 99, 99, 99, 99, 99, 99, 127, 127, 99, 1, 1, 1, 1, 1, 7, 7, 1, 1, 21, 21, 21, 21, 21, 41, 99, 99, 99, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 170 rigid atoms, others: [33, 2, 41, 42, 34, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 372 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: REAL300000082477 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 29, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 99, 99, 39, 99, 150, 150, 99, 99, 56, 56, 56, 56, 56, 7, 1, 1, 1, 99, 99, 150, 150, 150, 150, 150, 150, 99, 99] 170 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 653 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082477 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082477 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082477/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082477 Building REAL300000082478 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082478' /scratch/stefan/7930160/working/building/REAL300000082478 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082478 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082478/0 /scratch/stefan/7930160/working/building/REAL300000082478 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/506 `/scratch/stefan/7930160/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1N(C)C) `REAL300000082478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082478 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 16, 43, 43, 43, 1, 1, 1, 4, 4, 4, 4, 4, 4] 43 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 93 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: REAL300000082478 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 43, 43, 42, 43, 43, 43, 43, 43, 43, 30, 30, 30, 9, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 43 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 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: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082478 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082478 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082478/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082478 Building REAL300000082479 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082479' /scratch/stefan/7930160/working/building/REAL300000082479 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082479 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082479/0 /scratch/stefan/7930160/working/building/REAL300000082479 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/507 `/scratch/stefan/7930160/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CCC2=CC=CC=C2)=CC=C1F) `REAL300000082479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082479 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CCC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 133, 151, 133, 133, 59, 59, 17, 4, 3, 1, 1, 1, 1, 1, 1, 1, 16, 45, 51, 61, 61, 57, 61, 61, 133, 133, 133, 133, 133, 17, 4, 4, 3, 3, 1, 1, 1, 1, 1, 45, 45, 51, 51, 61, 61, 61, 61, 61, 133, 133] 201 rigid atoms, others: [35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 490 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082479 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CCC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 43, 92, 113, 133, 133, 120, 133, 133, 43, 93, 114, 132, 132, 124, 132, 132, 1, 1, 1, 1, 1, 43, 102, 102, 109, 113, 133, 133, 133, 133, 133, 103, 103, 114, 110, 132, 132, 132, 132, 132, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 49, 50, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1048 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082479 none O=C([O-])C1=CC(N=NC(CCC2=CC=CC=C2)CCC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 132, 150, 132, 132, 57, 57, 17, 4, 17, 45, 51, 61, 61, 53, 61, 61, 3, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 17, 45, 45, 51, 51, 61, 61, 61, 61, 61, 4, 4, 3, 3, 1, 1, 1, 1, 1, 132, 132] 201 rigid atoms, others: [44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50]) total number of confs: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082479 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082479 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082479/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082479 Building REAL300000082480 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082480' /scratch/stefan/7930160/working/building/REAL300000082480 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082480 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082480/0 /scratch/stefan/7930160/working/building/REAL300000082480 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/508 `/scratch/stefan/7930160/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(C)(C)C2=C1) `REAL300000082480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082480 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [11, 1, 11, 11, 64, 176, 176, 176, 176, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 176, 176, 176, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 176 rigid atoms, others: [1, 34, 35, 33, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 320 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082480 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 52, 52, 52, 10, 1, 1, 1, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176] 176 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082480 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082480 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082480/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082480 Building REAL300000082481 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082481' /scratch/stefan/7930160/working/building/REAL300000082481 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082481 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082481/0 /scratch/stefan/7930160/working/building/REAL300000082481 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/509 `/scratch/stefan/7930160/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(C(C)(C)C)=N2)C=C1) `REAL300000082481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082481 none CC1=CC=C(N2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(C(C)(C)C)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 24, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 3, 3, 3, 1, 3, 3, 4, 4, 4, 4, 4, 1, 8, 24, 52, 52, 52, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 52 rigid atoms, others: [34, 4, 5, 6, 7, 8, 21, 22, 26] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082481 none CC1=CC=C(N2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(C(C)(C)C)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 5, 13, 13, 37, 52, 52, 52, 52, 52, 52, 52, 52, 52, 4, 5, 6, 6, 6, 4, 1, 1, 2, 2, 2, 1, 1, 5, 13, 37, 52, 52, 52, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 52 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082481 none CC1=CC=C(N2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(C(C)(C)C)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 34, 8, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52] 52 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082481 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082481 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082481/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082481 Building REAL300000082482 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082482' /scratch/stefan/7930160/working/building/REAL300000082482 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082482 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082482/0 /scratch/stefan/7930160/working/building/REAL300000082482 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/510 `/scratch/stefan/7930160/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1O) `REAL300000082482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082482 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [11, 1, 11, 11, 51, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 101, 101, 101, 1, 1, 1, 2] 202 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 201 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: REAL300000082482 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 101, 101, 87, 101, 101, 101, 101, 49, 49, 49, 11, 1, 1, 1, 101, 101, 101, 202] 202 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 424 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082482 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082482 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082482/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082482 Building REAL300000082483 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082483' /scratch/stefan/7930160/working/building/REAL300000082483 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082483 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082483/0 /scratch/stefan/7930160/working/building/REAL300000082483 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/511 `/scratch/stefan/7930160/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(OCC(F)(F)F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082483 none CC1=NN(C)C(OCC(F)(F)F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [88, 88, 88, 88, 88, 88, 88, 147, 201, 201, 201, 201, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 88, 88, 88, 88, 88, 88, 201, 201, 23, 5, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082483 none CC1=NN(C)C(OCC(F)(F)F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7, 25, 25, 25, 25, 1, 1, 12, 12, 47, 88, 88, 88, 88, 88, 88, 116, 116, 88, 2, 2, 2, 2, 2, 2, 25, 25, 12, 47, 88, 88, 88] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13] set([7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082483 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082483 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082483/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082483 Building REAL300000082484 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082484' /scratch/stefan/7930160/working/building/REAL300000082484 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082484 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082484/0 /scratch/stefan/7930160/working/building/REAL300000082484 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/512 `/scratch/stefan/7930160/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2) `REAL300000082484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082484 none CCC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 43, 43, 43, 43, 43, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 88, 88, 88, 88, 88, 11, 1, 1, 1, 43, 43, 43, 43, 43, 43] 88 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082484 none CCC1=NC2=C(S1)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 43, 43, 43, 43, 69, 69, 43, 1, 1, 1, 9, 9, 9, 8, 8, 7, 43, 43, 43, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 20, 21, 22, 36, 33, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082484 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082484/1 /scratch/stefan/7930160/working/building/REAL300000082484 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/513 `/scratch/stefan/7930160/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2) `REAL300000082484.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082484 none CCC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 55, 55, 55, 55, 55, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 55, 55, 94, 94, 94, 94, 94, 55, 1, 1, 1, 55, 55, 55, 55, 55, 55] 94 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) 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: REAL300000082484 none CCC1=NC2=C(S1)C(N=NC1=CC=C(F)C(C(=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 55, 55, 75, 75, 55, 1, 1, 1, 9, 9, 9, 8, 8, 1, 55, 55, 55, 1, 1, 1, 1, 1, 1] 94 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 36, 33, 28, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082484 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082484 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082484/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082484/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082484 Building REAL300000082485 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082485' /scratch/stefan/7930160/working/building/REAL300000082485 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082485 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082485/0 /scratch/stefan/7930160/working/building/REAL300000082485 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/514 `/scratch/stefan/7930160/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082485 none COC1=CC=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 39, 110, 110, 110, 110, 110, 110, 134, 134, 110, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 3, 7, 39, 110, 110, 110] 134 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) 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: REAL300000082485 none COC1=CC=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 24, 76, 76, 76, 76, 76, 76, 111, 111, 76, 4, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 4, 24, 76, 76, 76] 134 rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 37, 30, 31] set([0, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082485 none COC1=CC=C(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [112, 76, 76, 76, 76, 76, 76, 110, 110, 76, 110, 110, 76, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 112, 112, 112, 76, 76, 110, 110, 76, 110, 110, 76, 39, 10, 1, 1, 1] 134 rigid atoms, others: [40, 41, 42, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 367 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082485 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082485 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082485/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082485 Building REAL300000082486 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082486' /scratch/stefan/7930160/working/building/REAL300000082486 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082486 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082486/0 /scratch/stefan/7930160/working/building/REAL300000082486 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/515 `/scratch/stefan/7930160/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C(F)=C1) `REAL300000082486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082486 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [12, 1, 12, 12, 63, 175, 175, 175, 175, 175, 175, 175, 175, 175, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 175, 175, 175, 1, 1, 1] 175 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 308 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: REAL300000082486 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [55, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 175, 175, 175, 175, 175, 175, 175, 56, 56, 56, 11, 1, 1, 1, 175, 175, 175] 175 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 258 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082486 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082486 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082486/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082486 Building REAL300000082487 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082487' /scratch/stefan/7930160/working/building/REAL300000082487 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082487 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082487/0 /scratch/stefan/7930160/working/building/REAL300000082487 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/516 `/scratch/stefan/7930160/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082487 none COC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 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, 108, 201, 108, 108, 108, 108, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 201, 201, 201, 108, 108, 108, 36, 9, 1, 1, 1, 108] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082487 none COC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 50, 108, 108, 108, 108, 108, 108, 140, 140, 107, 1, 13, 13, 13, 1, 1, 1, 11, 50, 108, 108, 108, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 34, 22, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082487 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082487 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082487/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082487 Building REAL300000082488 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082488' /scratch/stefan/7930160/working/building/REAL300000082488 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082488 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082488/0 /scratch/stefan/7930160/working/building/REAL300000082488 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/517 `/scratch/stefan/7930160/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1F) `REAL300000082488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082488 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [11, 1, 11, 11, 58, 124, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 124, 124, 124, 1, 1, 1] 124 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000082488 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [49, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 124, 124, 64, 124, 124, 124, 124, 50, 50, 50, 11, 1, 1, 1, 124, 124, 124] 124 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 421 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082488 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082488 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082488/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082488 Building REAL300000082489 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082489' /scratch/stefan/7930160/working/building/REAL300000082489 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082489 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082489/0 /scratch/stefan/7930160/working/building/REAL300000082489 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/518 `/scratch/stefan/7930160/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=CC3=CC=CN=C23)=CC=C1F) `REAL300000082489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082489 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 26, 4, 1, 1, 1, 1, 1, 56, 56] 56 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082489 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 11, 42, 42, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 11, 42, 56, 56, 56, 56, 56, 1, 1] 56 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082489 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082489 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082489/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082489 Building REAL300000082490 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082490' /scratch/stefan/7930160/working/building/REAL300000082490 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082490 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082490/0 /scratch/stefan/7930160/working/building/REAL300000082490 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/519 `/scratch/stefan/7930160/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C3=CC=CN=C23)=CC=C1F) `REAL300000082490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082490 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 24, 4, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082490 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 46, 46, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 10, 46, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082490 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082490 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082490/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082490 Building REAL300000082491 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082491' /scratch/stefan/7930160/working/building/REAL300000082491 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082491 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082491/0 /scratch/stefan/7930160/working/building/REAL300000082491 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/520 `/scratch/stefan/7930160/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(C(F)(F)F)=CC=C21) `REAL300000082491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082491 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(C(F)(F)F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 59, 13, 1, 1, 1, 102, 102, 102] 102 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082491 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(C(F)(F)F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 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, 12, 12, 44, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 12, 44, 102, 102, 102, 1, 1, 1] 102 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 16, 17, 18, 19, 20, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082491 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082491/1 /scratch/stefan/7930160/working/building/REAL300000082491 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/521 `/scratch/stefan/7930160/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(C(F)(F)F)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082491.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082491 none CN1C2=CC=C(C(F)(F)F)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 155, 155, 155, 154, 154, 154, 51, 51, 1, 1, 1] 155 rigid atoms, others: [35, 36, 37, 16, 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, 24, 25, 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: REAL300000082491 none CN1C2=CC=C(C(F)(F)F)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 8, 64, 64, 154, 154, 154, 154, 154, 154, 155, 155, 154, 2, 2, 2, 1, 1, 1, 8, 8, 154, 154, 154] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 32, 30, 31] set([33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082491 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082491 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082491/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082491/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082491 Building REAL300000082492 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082492' /scratch/stefan/7930160/working/building/REAL300000082492 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082492 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082492/0 /scratch/stefan/7930160/working/building/REAL300000082492 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/522 `/scratch/stefan/7930160/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C) `REAL300000082492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082492 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 53, 53, 121, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 121, 121, 121, 1, 1, 1, 2, 2, 2] 121 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 191 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: REAL300000082492 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 49, 49, 49, 49, 1, 1, 1, 121, 121, 121, 121, 121, 121] 121 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 260 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082492 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082492/1 /scratch/stefan/7930160/working/building/REAL300000082492 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/523 `/scratch/stefan/7930160/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C) `REAL300000082492.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082492 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 31, 69, 69, 68, 68, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 31, 69, 69, 69, 1, 1, 1, 2, 2, 2] 69 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082492 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=CC=C(Cl)C=C2N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 47, 47, 47, 13, 1, 1, 1, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082492 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082492 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082492/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082492/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082492 Building REAL300000082493 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082493' /scratch/stefan/7930160/working/building/REAL300000082493 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082493 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082493/0 /scratch/stefan/7930160/working/building/REAL300000082493 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/524 `/scratch/stefan/7930160/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1) `REAL300000082493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082493 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [21, 19, 22, 7, 1, 7, 7, 32, 110, 110, 110, 110, 110, 110, 128, 128, 109, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 19, 19, 32, 110, 110, 109, 1, 1, 1, 1] 138 rigid atoms, others: [4, 37, 38, 39, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 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]) total number of confs: 326 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: REAL300000082493 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [103, 97, 104, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 109, 109, 109, 109, 109, 104, 104, 104, 104, 104, 104, 104, 97, 97, 10, 1, 1, 1, 110, 110, 109, 109] 138 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 455 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082493 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082493/1 /scratch/stefan/7930160/working/building/REAL300000082493 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/525 `/scratch/stefan/7930160/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1) `REAL300000082493.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082493 none CC(C)CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 30, 11, 1, 11, 60, 60, 158, 158, 158, 158, 158, 158, 160, 160, 158, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 27, 27, 11, 158, 158, 158, 1, 1, 1, 1] 161 rigid atoms, others: [4, 37, 38, 39, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 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]) total number of confs: 337 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082493 none CC(C)CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [68, 66, 68, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 158, 158, 158, 158, 158, 68, 68, 68, 68, 68, 68, 68, 66, 66, 49, 1, 1, 1, 158, 158, 158, 158] 161 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082493 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082493 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082493/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082493/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082493 Building REAL300000082494 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082494' /scratch/stefan/7930160/working/building/REAL300000082494 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082494 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082494/0 /scratch/stefan/7930160/working/building/REAL300000082494 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/526 `/scratch/stefan/7930160/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1Br) `REAL300000082494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082494 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [25, 9, 1, 9, 9, 41, 143, 143, 143, 143, 143, 143, 151, 151, 143, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 41, 143, 143, 143, 1, 1, 1, 1] 161 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 324 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082494 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [106, 44, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 143, 143, 81, 143, 143, 143, 106, 106, 106, 106, 106, 9, 1, 1, 1, 143, 143, 87, 143] 161 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 661 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082494 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082494 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082494/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082494 Building REAL300000082495 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082495' /scratch/stefan/7930160/working/building/REAL300000082495 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082495 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082495/0 /scratch/stefan/7930160/working/building/REAL300000082495 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/527 `/scratch/stefan/7930160/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)SC(Cl)=C32)=CC=C1F) `REAL300000082495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082495 none O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)SC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', '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, 1, 8, 8, 1, 5, 5, 5, 1, 1, 16, 14, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 43, 43] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 61 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: REAL300000082495 none O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)SC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', '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, 1, 8, 8, 1, 5, 5, 5, 1, 1, 16, 14, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 10, 43, 43, 43, 43, 43, 43, 1, 1] 43 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082495 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082495 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082495/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082495 Building REAL300000082496 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082496' /scratch/stefan/7930160/working/building/REAL300000082496 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082496 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082496/0 /scratch/stefan/7930160/working/building/REAL300000082496 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/528 `/scratch/stefan/7930160/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=C(F)C=CC=C23)=CC=C1F) `REAL300000082496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082496 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 32, 32, 33, 7, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082496 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C(F)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 33, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 13, 32, 33, 33, 33, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082496 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082496 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082496/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082496 Building REAL300000082497 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082497' /scratch/stefan/7930160/working/building/REAL300000082497 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082497 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082497/0 /scratch/stefan/7930160/working/building/REAL300000082497 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/529 `/scratch/stefan/7930160/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1O) `REAL300000082497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082497 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 254 conformations in input total number of sets (complete confs): 254 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 63, 127, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 127, 127, 127, 1, 1, 2] 254 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 249 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: REAL300000082497 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 254 conformations in input total number of sets (complete confs): 254 using faster count positions algorithm for large data unique positions, atoms: [47, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 127, 127, 127, 119, 127, 127, 127, 127, 48, 48, 48, 11, 1, 1, 1, 127, 127, 254] 254 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 488 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082497 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082497/1 /scratch/stefan/7930160/working/building/REAL300000082497 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/530 `/scratch/stefan/7930160/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1[O-]) `REAL300000082497.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082497 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082497 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(F)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [32, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 37, 37, 37, 37, 37, 37, 37, 37, 33, 33, 33, 9, 1, 1, 1, 37, 37] 37 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082497 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082497 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082497/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082497/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082497 Building REAL300000082498 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082498' /scratch/stefan/7930160/working/building/REAL300000082498 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082498 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082498/0 /scratch/stefan/7930160/working/building/REAL300000082498 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/531 `/scratch/stefan/7930160/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082498 none CC1=CC(Cl)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 33, 33, 33, 32, 32, 32, 32, 32, 32, 32, 9, 1, 1, 1, 32] 33 rigid atoms, others: [36, 37, 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, 35, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082498 none CC1=CC(Cl)=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 32, 33, 33, 32, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 32, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 28, 29, 30, 31, 32, 33, 34, 39] set([35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082498 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082498 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082498/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082498 Building REAL300000082499 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082499' /scratch/stefan/7930160/working/building/REAL300000082499 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082499 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082499/0 /scratch/stefan/7930160/working/building/REAL300000082499 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/532 `/scratch/stefan/7930160/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Cl)=CC=C1F) `REAL300000082499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082499 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 31, 8, 1, 1, 1, 66, 66] 66 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082499 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 47, 47, 66, 66, 49, 66, 66, 66, 66, 1, 1, 1, 1, 1, 13, 47, 66, 66, 66, 1, 1] 66 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082499 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082499 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082499/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082499 Building REAL300000082500 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082500' /scratch/stefan/7930160/working/building/REAL300000082500 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082500 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082500/0 /scratch/stefan/7930160/working/building/REAL300000082500 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/533 `/scratch/stefan/7930160/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Br)=CC=C1F) `REAL300000082500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082500 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 34, 10, 1, 1, 1, 67, 67] 67 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082500 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 67, 67, 41, 49, 67, 67, 67, 1, 1, 1, 1, 1, 11, 41, 67, 67, 67, 1, 1] 67 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082500 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082500 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082500/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082500 Building REAL300000082501 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082501' /scratch/stefan/7930160/working/building/REAL300000082501 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082501 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082501/0 /scratch/stefan/7930160/working/building/REAL300000082501 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/534 `/scratch/stefan/7930160/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C=C2F)=CC=C1F) `REAL300000082501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082501 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 33, 9, 1, 1, 56, 56] 56 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000082501 none O=C([O-])C1=CC(NN=CC2=CC(F)=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 15, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 38, 38, 56, 56, 56, 55, 55, 56, 56, 56, 1, 1, 1, 1, 1, 10, 38, 56, 56, 1, 1] 56 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082501 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082501 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082501/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082501 Building REAL300000082502 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082502' /scratch/stefan/7930160/working/building/REAL300000082502 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082502 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082502/0 /scratch/stefan/7930160/working/building/REAL300000082502 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/535 `/scratch/stefan/7930160/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2Cl)=CC=C1F) `REAL300000082502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082502 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 38, 8, 1, 1, 1, 71, 71] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082502 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 40, 40, 71, 71, 71, 47, 71, 71, 71, 1, 1, 1, 1, 1, 10, 40, 71, 69, 71, 1, 1] 71 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: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082502 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082502 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082502/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082502 Building REAL300000082503 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082503' /scratch/stefan/7930160/working/building/REAL300000082503 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082503 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082503/0 /scratch/stefan/7930160/working/building/REAL300000082503 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/536 `/scratch/stefan/7930160/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2[N+](=O)[O-])=CC=C1F) `REAL300000082503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082503 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 38, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 99, 99, 99, 99, 99, 38, 7, 1, 1, 1, 99, 99] 99 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000082503 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 70, 70, 99, 99, 85, 90, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 13, 70, 99, 99, 99, 1, 1] 99 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082503 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082503 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082503/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082503 Building REAL300000082504 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082504' /scratch/stefan/7930160/working/building/REAL300000082504 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082504 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082504/0 /scratch/stefan/7930160/working/building/REAL300000082504 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/537 `/scratch/stefan/7930160/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=NN2)=CC=C1F) `REAL300000082504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=NN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 64, 87, 64, 64, 19, 7, 7, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 64, 64, 64, 64, 64, 19, 7, 1, 7, 7, 2, 7, 7, 1, 64, 64] 91 rigid atoms, others: [33, 8, 9, 10, 11, 12, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=NN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 44, 44, 64, 64, 64, 91, 91, 75, 91, 91, 64, 64, 1, 1, 1, 1, 1, 10, 44, 64, 91, 91, 88, 91, 91, 64, 1, 1] 91 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=CC(C3=CC=CC=C3)=NN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 54, 19, 19, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 91, 91, 91, 91, 91, 54, 19, 7, 1, 1, 1, 1, 1, 7, 91, 91] 91 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35]) total number of confs: 194 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082504 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082504/1 /scratch/stefan/7930160/working/building/REAL300000082504 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/538 `/scratch/stefan/7930160/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=C3)=C2)=CC=C1F) `REAL300000082504.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [65, 54, 65, 54, 54, 18, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 54, 54, 53, 53, 54, 18, 6, 1, 7, 7, 6, 7, 7, 1, 54, 54] 93 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 11, 44, 44, 54, 54, 54, 54, 93, 93, 87, 93, 93, 54, 1, 1, 1, 1, 1, 11, 44, 54, 93, 93, 93, 93, 93, 54, 1, 1] 93 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082504 none O=C([O-])C1=CC(NN=CC2=NNC(C3=CC=CC=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 54, 20, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 93, 93, 93, 93, 93, 54, 20, 7, 1, 1, 1, 1, 1, 7, 93, 93] 93 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082504 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082504 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082504/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082504/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082504 Building REAL300000082505 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082505' /scratch/stefan/7930160/working/building/REAL300000082505 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082505 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082505/0 /scratch/stefan/7930160/working/building/REAL300000082505 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/539 `/scratch/stefan/7930160/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2[N+](=O)[O-])C2CC2)=CC=C1F) `REAL300000082505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082505 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2[N+](=O)[O-])C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 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: [173, 150, 173, 150, 150, 63, 63, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 25, 25, 150, 150, 150, 150, 150, 11, 6, 6, 1, 1, 1, 1, 25, 25, 25, 25, 25, 150, 150] 174 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 379 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082505 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2[N+](=O)[O-])C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 1, 3, 1, 1, 1, 1, 8, 8, 50, 106, 150, 150, 106, 150, 150, 150, 150, 150, 50, 78, 78, 1, 1, 1, 1, 1, 50, 106, 106, 150, 150, 106, 150, 78, 78, 78, 78, 78, 1, 1] 174 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 728 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082505 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2[N+](=O)[O-])C2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 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: [115, 78, 115, 78, 78, 30, 30, 4, 1, 4, 15, 25, 25, 15, 25, 25, 25, 25, 25, 1, 1, 1, 78, 78, 78, 78, 78, 4, 15, 15, 25, 25, 15, 25, 1, 1, 1, 1, 1, 78, 78] 174 rigid atoms, others: [34, 35, 36, 37, 38, 8, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 342 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082505 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082505 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082505/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082505 Building REAL300000082506 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082506' /scratch/stefan/7930160/working/building/REAL300000082506 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082506 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082506/0 /scratch/stefan/7930160/working/building/REAL300000082506 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/540 `/scratch/stefan/7930160/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1F) `REAL300000082506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082506 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 188, 188, 86, 24, 24, 6, 3, 1, 1, 1, 1, 1, 1, 1, 24, 42, 42, 24, 42, 42, 188, 188, 188, 188, 188, 86, 6, 6, 3, 3, 1, 1, 1, 1, 1, 42, 42, 24, 42, 42, 188, 188] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082506 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 34, 160, 183, 188, 188, 186, 188, 188, 34, 66, 66, 34, 66, 66, 1, 1, 1, 1, 1, 8, 160, 160, 183, 183, 188, 188, 188, 188, 188, 66, 66, 34, 66, 66, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 810 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082506 none O=C([O-])C1=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 99, 66, 66, 21, 4, 4, 1, 4, 29, 35, 42, 42, 37, 42, 42, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 21, 29, 29, 35, 35, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 66, 66] 201 rigid atoms, others: [38, 39, 8, 41, 42, 17, 18, 19, 20, 21, 22, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 394 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082506 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082506 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082506/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082506 Building REAL300000082507 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082507' /scratch/stefan/7930160/working/building/REAL300000082507 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082507 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082507/0 /scratch/stefan/7930160/working/building/REAL300000082507 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/541 `/scratch/stefan/7930160/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OC) `REAL300000082507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082507 none CCC1(CC)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) 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: REAL300000082507 none CCC1(CC)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 34, 34, 34, 1, 1, 1, 4, 4, 4] 34 rigid atoms, others: [32, 1, 2, 3, 36, 5, 6, 18, 19, 20, 38, 37] set([0, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082507 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082507 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082507/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082507 Building REAL300000082508 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082508' /scratch/stefan/7930160/working/building/REAL300000082508 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082508 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082508/0 /scratch/stefan/7930160/working/building/REAL300000082508 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/542 `/scratch/stefan/7930160/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(O)=C(O)C(Br)=C2)=CC=C1F) `REAL300000082508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082508 none O=C([O-])C1=CC(NN=CC2=CC(O)=C(O)C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 66, 66, 67, 45, 9, 1, 2, 2, 1, 67, 67] 268 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 30]) total number of confs: 146 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082508 none O=C([O-])C1=CC(NN=CC2=CC(O)=C(O)C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 32, 32, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 10, 32, 67, 134, 134, 67, 1, 1] 268 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 379 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082508 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082508/1 /scratch/stefan/7930160/working/building/REAL300000082508 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/543 `/scratch/stefan/7930160/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(O)=C([O-])C(Br)=C2)=CC=C1F) `REAL300000082508.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082508 none O=C([O-])C1=CC(NN=CC2=CC(O)=C([O-])C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 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, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 45, 11, 1, 2, 1, 51, 51] 102 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 26, 28, 29]) 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: REAL300000082508 none O=C([O-])C1=CC(NN=CC2=CC(O)=C([O-])C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 12, 1, 12, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 4, 22, 22, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 4, 22, 51, 102, 51, 1, 1] 102 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082508 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082508 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082508/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082508/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082508 Building REAL300000082509 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082509' /scratch/stefan/7930160/working/building/REAL300000082509 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082509 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082509/0 /scratch/stefan/7930160/working/building/REAL300000082509 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/544 `/scratch/stefan/7930160/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1) `REAL300000082509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 54, 56, 56, 54, 56, 56, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 30, 30, 54, 54, 56, 56, 54, 56, 56] 56 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 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: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 30, 30, 30, 30, 30, 30, 32, 32, 30, 1, 1, 1, 1, 4, 5, 5, 4, 5, 5, 2, 2, 2, 1, 1, 1, 1, 30, 30, 30, 1, 1, 4, 4, 5, 5, 4, 5, 5] 56 rigid atoms, others: [0, 1, 2, 3, 4, 37, 32, 16, 17, 18, 19, 36, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 29, 29, 56, 56, 56, 56, 56, 56, 56, 56, 56, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 56, 56, 56, 5, 5, 2, 2, 1, 1, 1, 1, 1] 56 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 89 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082509 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082509/1 /scratch/stefan/7930160/working/building/REAL300000082509 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/545 `/scratch/stefan/7930160/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1) `REAL300000082509.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 34, 72, 86, 86, 72, 86, 86, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 34, 34, 72, 72, 86, 86, 72, 86, 86] 86 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 327 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: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 34, 34, 34, 34, 34, 34, 53, 53, 34, 1, 1, 1, 1, 4, 7, 7, 4, 7, 7, 2, 2, 2, 1, 1, 1, 1, 34, 34, 34, 1, 1, 4, 4, 7, 7, 4, 7, 7] 86 rigid atoms, others: [0, 1, 2, 3, 4, 37, 32, 16, 17, 18, 19, 36, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082509 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 50, 50, 86, 86, 86, 86, 86, 86, 86, 86, 86, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 86, 86, 86, 7, 7, 3, 3, 1, 1, 1, 1, 1] 86 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082509 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082509 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082509/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082509/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082509 Building REAL300000082510 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082510' /scratch/stefan/7930160/working/building/REAL300000082510 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082510 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082510/0 /scratch/stefan/7930160/working/building/REAL300000082510 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/546 `/scratch/stefan/7930160/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C3=CC=CN=C23)=CC=C1F) `REAL300000082510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082510 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 26, 6, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082510 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 42, 42, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 10, 42, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082510 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082510 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082510/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082510 Building REAL300000082511 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082511' /scratch/stefan/7930160/working/building/REAL300000082511 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082511 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082511/0 /scratch/stefan/7930160/working/building/REAL300000082511 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/547 `/scratch/stefan/7930160/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082511 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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 201 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, 159, 136, 159, 60, 60, 60, 60, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 60, 60, 20, 5, 1, 1, 1, 60] 201 rigid atoms, others: [41, 42, 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, 40, 44]) total number of confs: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082511 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 25, 27, 27, 13, 8, 13, 1, 1, 1, 1, 1, 1, 7, 7, 37, 60, 60, 60, 60, 60, 60, 91, 91, 60, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 1, 1, 7, 37, 60, 60, 60, 1] 201 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082511 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082511 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082511/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082511 Building REAL300000082512 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082512' /scratch/stefan/7930160/working/building/REAL300000082512 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082512 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082512/0 /scratch/stefan/7930160/working/building/REAL300000082512 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/548 `/scratch/stefan/7930160/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1) `REAL300000082512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082512 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 61, 61, 143, 143, 143, 143, 143, 143, 200, 200, 143, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 11, 11, 11, 11, 143, 143, 143, 1, 1, 6, 6, 2, 6, 6] 201 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082512 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 143, 143, 143, 143, 201, 201, 201, 201, 201, 143, 38, 38, 38, 38, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082512 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 6, 37, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 37, 37, 37, 37, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1] 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]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082512 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082512/1 /scratch/stefan/7930160/working/building/REAL300000082512 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/549 `/scratch/stefan/7930160/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1) `REAL300000082512.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082512 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 80, 80, 80, 80, 80, 80, 100, 100, 80, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 8, 8, 8, 26, 80, 80, 80, 1, 1, 7, 6, 1, 7, 6] 107 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) 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: REAL300000082512 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [43, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 80, 80, 80, 80, 107, 107, 80, 107, 107, 80, 44, 44, 44, 11, 1, 1, 1, 80, 80, 107, 107, 80, 107, 107] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 273 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082512 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 25, 66, 107, 107, 107, 107, 107, 107, 107, 107, 107, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 66, 107, 107, 107, 6, 7, 1, 1, 1, 1, 1] 107 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]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082512 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082512 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082512/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082512/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082512 Building REAL300000082513 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082513' /scratch/stefan/7930160/working/building/REAL300000082513 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082513 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082513/0 /scratch/stefan/7930160/working/building/REAL300000082513 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/550 `/scratch/stefan/7930160/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CSC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082513 none NC(=O)C1=CSC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [8, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 74, 102, 74, 74, 74, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 74, 102, 102, 74, 48, 10, 1, 1, 1, 74] 102 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29]) 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: REAL300000082513 none NC(=O)C1=CSC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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: [8, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 39, 74, 74, 74, 74, 74, 74, 76, 76, 74, 1, 3, 3, 1, 8, 39, 74, 74, 74, 1] 102 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082513 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082513 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082513/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082513 Building REAL300000082514 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082514' /scratch/stefan/7930160/working/building/REAL300000082514 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082514 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082514/0 /scratch/stefan/7930160/working/building/REAL300000082514 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/551 `/scratch/stefan/7930160/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082514 none COC(=O)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 164, 176, 118, 168, 168, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 168, 168, 176, 176, 176, 168, 168, 47, 47, 47, 10, 1, 1, 1, 168, 168] 176 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 477 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082514 none COC(=O)C1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 13, 66, 168, 168, 168, 168, 168, 168, 173, 173, 168, 1, 1, 7, 7, 7, 1, 1, 13, 13, 13, 66, 168, 168, 168, 1, 1] 176 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 36, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 335 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082514 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082514 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082514/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082514 Building REAL300000082515 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082515' /scratch/stefan/7930160/working/building/REAL300000082515 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082515 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082515/0 /scratch/stefan/7930160/working/building/REAL300000082515 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/552 `/scratch/stefan/7930160/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(O)=C3O)=CC=C1F) `REAL300000082515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082515 none O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(O)=C3O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 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: [44, 43, 44, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 2, 2, 43, 43] 176 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 34, 19, 20, 21, 22, 23, 24, 33, 31]) total number of confs: 70 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: REAL300000082515 none O=C([O-])C1=CC(NN=C2CCC3=C2C=CC(O)=C3O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 86, 86, 1, 1] 176 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 239 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082515 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082515 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082515/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082515 Building REAL300000082516 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082516' /scratch/stefan/7930160/working/building/REAL300000082516 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082516 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082516/0 /scratch/stefan/7930160/working/building/REAL300000082516 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/553 `/scratch/stefan/7930160/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl) `REAL300000082516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082516 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 1, 9, 9, 46, 177, 177, 177, 177, 177, 177, 181, 181, 177, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 46, 177, 177, 177, 1, 1, 1] 187 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 366 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082516 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [116, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 177, 177, 177, 94, 177, 177, 177, 116, 116, 116, 116, 116, 10, 1, 1, 1, 177, 174, 177] 187 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 899 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082516 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082516 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082516/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082516 Building REAL300000082517 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082517' /scratch/stefan/7930160/working/building/REAL300000082517 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082517 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082517/0 /scratch/stefan/7930160/working/building/REAL300000082517 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/554 `/scratch/stefan/7930160/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCCC(C)C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082517 none COC(=O)CCCCC(C)C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 107, 201, 54, 53, 53, 27, 15, 29, 5, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 107, 107, 54, 54, 53, 53, 53, 53, 29, 29, 29, 29, 15, 15, 15, 15, 1, 1, 1] 201 rigid atoms, others: [45, 43, 44, 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, 38, 39, 40, 41, 42]) total number of confs: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082517 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082517 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082517/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082517 Building REAL300000082518 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082518' /scratch/stefan/7930160/working/building/REAL300000082518 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082518 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082518/0 /scratch/stefan/7930160/working/building/REAL300000082518 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/555 `/scratch/stefan/7930160/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(=O)N1CC1=CC=CC=C1) `REAL300000082518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082518 none CC1C(NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(=O)N1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 84, 84, 84, 84, 84, 153, 201, 201, 199, 201, 201, 84, 84, 84, 84, 33, 10, 1, 1, 1, 84, 153, 153, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 601 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: REAL300000082518 none CC1C(NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(=O)N1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 25, 84, 84, 84, 84, 84, 84, 129, 129, 84, 1, 1, 1, 1, 1, 6, 9, 9, 8, 9, 9, 2, 2, 2, 1, 7, 25, 84, 84, 84, 1, 6, 6, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 19, 15, 16, 17, 18, 35, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 354 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082518 none CC1C(NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(=O)N1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 32, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 83, 201, 201, 201, 9, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 396 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082518 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082518 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082518/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082518 Building REAL300000082519 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082519' /scratch/stefan/7930160/working/building/REAL300000082519 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082519 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082519/0 /scratch/stefan/7930160/working/building/REAL300000082519 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/556 `/scratch/stefan/7930160/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3CCCC3)N=C2)=CC=C1F) `REAL300000082519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082519 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCCC3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [101, 80, 101, 80, 80, 47, 9, 9, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 80, 80, 80, 80, 80, 47, 9, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 80, 80] 123 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082519 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCCC3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 31, 31, 79, 80, 80, 80, 123, 123, 123, 123, 80, 80, 1, 1, 1, 1, 1, 7, 31, 80, 80, 123, 123, 123, 123, 123, 123, 123, 123, 80, 1, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082519 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCCC3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 96, 35, 35, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 122, 122, 122, 122, 122, 96, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 122, 122] 122 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39]) total number of confs: 289 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082519 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082519 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082519/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082519 Building REAL300000082520 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082520' /scratch/stefan/7930160/working/building/REAL300000082520 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082520 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082520/0 /scratch/stefan/7930160/working/building/REAL300000082520 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/557 `/scratch/stefan/7930160/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082520 none CC(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 70, 114, 70, 70, 70, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 70, 114, 114, 114, 114, 114, 114, 114, 70, 33, 9, 1, 1, 1] 114 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000082520 none CC(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 36, 70, 70, 70, 70, 70, 70, 101, 101, 70, 1, 13, 13, 13, 12, 13, 13, 13, 1, 8, 35, 70, 70, 70] 114 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082520 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082520 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082520/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082520 Building REAL300000082521 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082521' /scratch/stefan/7930160/working/building/REAL300000082521 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082521 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082521/0 /scratch/stefan/7930160/working/building/REAL300000082521 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/558 `/scratch/stefan/7930160/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082521 none CC(C)C1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 40, 58, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 40, 58, 58, 58, 58, 58, 58, 58, 40, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 40] 58 rigid atoms, others: [42, 43, 44, 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, 38, 39, 40, 41, 45]) 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: REAL300000082521 none CC(C)C1=CC=C2OCCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 39, 39, 40, 40, 55, 55, 40, 1, 1, 4, 4, 4, 4, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 40, 1] 58 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 45] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082521 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082521 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082521/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082521 Building REAL300000082522 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082522' /scratch/stefan/7930160/working/building/REAL300000082522 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082522 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082522/0 /scratch/stefan/7930160/working/building/REAL300000082522 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/559 `/scratch/stefan/7930160/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082522 none CC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 31, 54, 54, 54, 140, 201, 201, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 54, 54, 54, 54, 201, 30, 6, 1, 1, 1, 54] 201 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082522 none CC1=CC=C(OC(F)F)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 9, 45, 45, 1, 1, 4, 4, 22, 54, 54, 54, 54, 54, 54, 89, 89, 54, 1, 2, 2, 2, 1, 1, 45, 4, 22, 54, 54, 54, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 35, 23, 27, 28] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082522 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082522 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082522/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082522 Building REAL300000082523 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082523' /scratch/stefan/7930160/working/building/REAL300000082523 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082523 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082523/0 /scratch/stefan/7930160/working/building/REAL300000082523 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/560 `/scratch/stefan/7930160/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082523 none COC1=CC(F)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 119, 119, 119, 119, 119, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 195, 179, 179, 179, 119, 32, 32, 32, 6, 1, 1, 1, 119, 195, 195, 195] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 417 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082523 none COC1=CC(F)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 12, 12, 12, 51, 119, 119, 119, 119, 119, 119, 159, 159, 119, 1, 1, 1, 3, 3, 3, 3, 1, 12, 12, 12, 51, 119, 119, 119, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 393 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082523 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082523 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082523/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082523 Building REAL300000082524 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082524' /scratch/stefan/7930160/working/building/REAL300000082524 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082524 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082524/0 /scratch/stefan/7930160/working/building/REAL300000082524 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/561 `/scratch/stefan/7930160/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3S2)=CC=C1F) `REAL300000082524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082524 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 44, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 44, 9, 1, 1, 1, 1, 1, 79, 79] 79 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082524 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 45, 45, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 11, 45, 79, 79, 79, 79, 79, 1, 1] 79 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082524 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082524 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082524/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082524 Building REAL300000082525 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082525' /scratch/stefan/7930160/working/building/REAL300000082525 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082525 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082525/0 /scratch/stefan/7930160/working/building/REAL300000082525 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/562 `/scratch/stefan/7930160/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082525 none COC(=O)C(C)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 133, 201, 87, 133, 44, 29, 44, 44, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 201, 201, 201, 133, 133, 133, 133, 44, 44, 18, 5, 1, 1, 1, 44, 44] 201 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 682 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082525 none COC(=O)C(C)OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [31, 31, 14, 31, 6, 14, 1, 1, 1, 1, 1, 1, 7, 7, 24, 44, 44, 44, 44, 44, 44, 62, 62, 44, 1, 1, 31, 31, 31, 14, 14, 14, 14, 1, 1, 7, 24, 44, 44, 44, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 257 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082525 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082525 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082525/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082525 Building REAL300000082526 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082526' /scratch/stefan/7930160/working/building/REAL300000082526 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082526 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082526/0 /scratch/stefan/7930160/working/building/REAL300000082526 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/563 `/scratch/stefan/7930160/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082526 none CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 31, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 4, 10, 31, 48, 48, 48] 48 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 115 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: REAL300000082526 none CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 8, 8, 27, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 2, 4, 4, 1, 8, 27, 48, 48, 48] 48 rigid atoms, others: [1, 4, 5, 6, 7, 42, 13, 14, 15] set([0, 2, 3, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082526 none CC(C)(C)C1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 8, 1, 1, 1] 48 rigid atoms, others: [45, 46, 47, 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]) total number of confs: 76 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082526 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082526 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082526/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082526 Building REAL300000082527 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082527' /scratch/stefan/7930160/working/building/REAL300000082527 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082527 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082527/0 /scratch/stefan/7930160/working/building/REAL300000082527 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/564 `/scratch/stefan/7930160/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082527 none COC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 4, 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] 1 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: [88, 56, 56, 56, 56, 56, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 90, 88, 88, 88, 56, 112, 36, 10, 1, 1, 1, 56, 90, 90, 90] 200 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 332 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082527 none COC1=CC(O)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 4, 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] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 56, 56, 56, 56, 56, 56, 80, 80, 56, 1, 1, 1, 3, 4, 4, 4, 1, 2, 6, 18, 56, 56, 56, 1, 3, 3, 3] 200 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 20, 21, 22, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 202 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082527 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082527 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082527/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082527 Building REAL300000082528 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082528' /scratch/stefan/7930160/working/building/REAL300000082528 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082528 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082528/0 /scratch/stefan/7930160/working/building/REAL300000082528 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/565 `/scratch/stefan/7930160/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082528 none CCCOC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 157, 66, 66, 66, 66, 66, 66, 66, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 201, 201, 201, 201, 201, 161, 161, 66, 66, 66, 66, 25, 7, 1, 1, 1, 66] 201 rigid atoms, others: [39, 40, 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, 38, 42]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082528 none CCCOC1=CC=C2NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 66, 66, 66, 66, 66, 66, 96, 96, 66, 1, 1, 25, 25, 25, 24, 24, 10, 10, 1, 1, 1, 1, 6, 28, 66, 66, 66, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 24, 25, 42, 36] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082528 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082528 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082528/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082528 Building REAL300000082529 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082529' /scratch/stefan/7930160/working/building/REAL300000082529 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082529 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082529/0 /scratch/stefan/7930160/working/building/REAL300000082529 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/566 `/scratch/stefan/7930160/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)OC3=CC=CC=C32)=CC=C1F) `REAL300000082529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082529 none O=C([O-])C1=CC(NN=CC2=C(Cl)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 110, 109, 109, 110, 65, 12, 1, 1, 1, 1, 110, 110] 110 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000082529 none O=C([O-])C1=CC(NN=CC2=C(Cl)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 51, 51, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 13, 51, 110, 110, 110, 110, 1, 1] 110 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082529 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082529 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082529/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082529 Building REAL300000082530 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082530' /scratch/stefan/7930160/working/building/REAL300000082530 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082530 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082530/0 /scratch/stefan/7930160/working/building/REAL300000082530 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/567 `/scratch/stefan/7930160/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1F) `REAL300000082530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082530 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 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, 159, 159, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 159, 159, 159, 159, 201, 201, 201, 159, 60, 12, 1, 1, 1, 159, 159] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082530 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 59, 159, 159, 159, 159, 159, 159, 201, 201, 159, 1, 1, 1, 1, 4, 4, 4, 1, 12, 59, 159, 159, 159, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082530 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082530 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082530/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082530 Building REAL300000082531 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082531' /scratch/stefan/7930160/working/building/REAL300000082531 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082531 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082531/0 /scratch/stefan/7930160/working/building/REAL300000082531 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/568 `/scratch/stefan/7930160/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=C1C(C)CC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082531 none CC1=CC=CC2=C1C(C)CC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1] 29 rigid atoms, others: [36, 37, 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, 35]) total number of confs: 53 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082531 none CC1=CC=CC2=C1C(C)CC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 33, 26, 27, 28, 29] set([32, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 52 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082531 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082531 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082531/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082531 Building REAL300000082532 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082532' /scratch/stefan/7930160/working/building/REAL300000082532 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082532 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082532/0 /scratch/stefan/7930160/working/building/REAL300000082532 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/569 `/scratch/stefan/7930160/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CC3(CCCCC3)OC3=CC=CC=C32)=CC=C1F) `REAL300000082532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082532 none O=C([O-])C1=CC(NN=C2CC3(CCCCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 45, 46, 23, 24, 25, 26, 27, 28]) total number of confs: 63 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082532 none O=C([O-])C1=CC(NN=C2CC3(CCCCC3)OC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 45, 46, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082532 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082532 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082532/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082532 Building REAL300000082533 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082533' /scratch/stefan/7930160/working/building/REAL300000082533 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082533 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082533/0 /scratch/stefan/7930160/working/building/REAL300000082533 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/570 `/scratch/stefan/7930160/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1N(C)C) `REAL300000082533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082533 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 39, 39, 39, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 39 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082533 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [26, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 9, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082533 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082533 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082533/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082533 Building REAL300000082534 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082534' /scratch/stefan/7930160/working/building/REAL300000082534 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082534 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082534/0 /scratch/stefan/7930160/working/building/REAL300000082534 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/571 `/scratch/stefan/7930160/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC2=CC=CC=C2)=CC=C1F) `REAL300000082534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082534 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [113, 86, 113, 86, 86, 54, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 8, 14, 14, 86, 86, 86, 86, 86, 54, 12, 1, 1, 1, 14, 14, 8, 14, 14, 86, 86] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082534 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 20, 20, 86, 86, 86, 36, 86, 86, 86, 167, 201, 201, 167, 201, 201, 1, 1, 1, 1, 1, 4, 20, 86, 86, 86, 201, 201, 179, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082534 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2OC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 141, 76, 76, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 76, 14, 14, 14, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082534 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082534 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082534/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082534 Building REAL300000082535 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082535' /scratch/stefan/7930160/working/building/REAL300000082535 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082535 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082535/0 /scratch/stefan/7930160/working/building/REAL300000082535 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/572 `/scratch/stefan/7930160/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2[N+](=O)[O-])=CC=C1F) `REAL300000082535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082535 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [71, 46, 71, 46, 46, 13, 13, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 5, 10, 10, 10, 10, 10, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 5, 10, 46, 46] 126 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 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: REAL300000082535 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 1, 3, 1, 1, 1, 1, 8, 8, 46, 46, 46, 46, 46, 96, 126, 126, 96, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 96, 96, 126, 126, 96, 126, 1, 1] 126 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 483 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082535 none O=C([O-])C1=CC(N=NC2CCCC2CC2=CC=CC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 56, 56, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 126, 126, 126, 126, 126, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 126, 126] 126 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 203 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082535 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082535 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082535/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082535 Building REAL300000082536 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082536' /scratch/stefan/7930160/working/building/REAL300000082536 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082536 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082536/0 /scratch/stefan/7930160/working/building/REAL300000082536 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/573 `/scratch/stefan/7930160/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(C)NC(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082536 none CC(CC(C)NC(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 13, 16, 21, 19, 23, 26, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 13, 13, 13, 18, 18, 21, 21, 21, 21, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 46, 24, 47, 21] 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, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082536 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082536 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082536/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082536 Building REAL300000082537 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082537' /scratch/stefan/7930160/working/building/REAL300000082537 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082537 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082537/0 /scratch/stefan/7930160/working/building/REAL300000082537 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/574 `/scratch/stefan/7930160/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C(F)F)=CC=C1F) `REAL300000082537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082537 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 134, 188, 133, 134, 47, 47, 8, 3, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 134, 134, 134, 134, 134, 8, 3, 3, 1, 1, 1, 1, 1, 29, 134, 134] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082537 none O=C([O-])C1=CC(N=NC(CC2=CC=CC=C2)C(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 57, 127, 134, 134, 128, 134, 134, 57, 142, 142, 1, 1, 1, 1, 1, 57, 127, 127, 134, 134, 134, 134, 134, 142, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 893 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082537 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082537 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082537/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082537 Building REAL300000082538 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082538' /scratch/stefan/7930160/working/building/REAL300000082538 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082538 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082538/0 /scratch/stefan/7930160/working/building/REAL300000082538 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/575 `/scratch/stefan/7930160/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1C) `REAL300000082538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082538 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 101, 101, 101, 1, 1, 2, 2, 1, 2, 2, 2] 101 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082538 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 101, 101, 47, 51, 101, 101, 101, 47, 47, 47, 11, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 101] 101 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 428 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082538 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082538 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082538/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082538 Building REAL300000082539 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082539' /scratch/stefan/7930160/working/building/REAL300000082539 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082539 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082539/0 /scratch/stefan/7930160/working/building/REAL300000082539 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/576 `/scratch/stefan/7930160/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(C)(C)C)=N1) `REAL300000082539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082539 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 54, 12, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 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: REAL300000082539 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 41, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 3, 3, 3, 1, 2, 2, 2, 1, 8, 41, 82, 82, 82, 3, 3, 3, 3, 3, 3, 3, 3, 3] 82 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082539 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082539 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082539/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082539 Building REAL300000082540 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082540' /scratch/stefan/7930160/working/building/REAL300000082540 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082540 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082540/0 /scratch/stefan/7930160/working/building/REAL300000082540 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/577 `/scratch/stefan/7930160/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)OC(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082540 none CC1=NN(CC(=O)OC(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 12, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 72, 190, 190, 190, 201, 201, 38, 38, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 38, 38, 72, 72, 201, 201, 201, 201, 201, 201, 201, 38, 38, 38, 17, 5, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082540 none CC1=NN(CC(=O)OC(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 12, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 42, 42, 47, 71, 71, 1, 1, 1, 1, 8, 8, 23, 38, 38, 38, 38, 38, 38, 48, 48, 38, 2, 2, 2, 6, 6, 71, 71, 71, 71, 71, 71, 71, 2, 2, 2, 8, 23, 38, 38, 38] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082540 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082540 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082540/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082540 Building REAL300000082541 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082541' /scratch/stefan/7930160/working/building/REAL300000082541 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082541 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082541/0 /scratch/stefan/7930160/working/building/REAL300000082541 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/578 `/scratch/stefan/7930160/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082541 none CC(C)COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 136, 54, 54, 54, 54, 54, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 201, 201, 201, 201, 201, 201, 201, 159, 159, 54, 54, 54, 22, 7, 1, 1, 1, 54] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37, 41]) total number of confs: 598 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: REAL300000082541 none CC(C)COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 54, 54, 54, 54, 54, 54, 79, 79, 54, 1, 21, 21, 21, 21, 21, 21, 21, 13, 13, 1, 1, 1, 6, 25, 54, 54, 54, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 290 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082541 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082541 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082541/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082541 Building REAL300000082542 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082542' /scratch/stefan/7930160/working/building/REAL300000082542 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082542 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082542/0 /scratch/stefan/7930160/working/building/REAL300000082542 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/579 `/scratch/stefan/7930160/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(Br)=C23)=CC=C1F) `REAL300000082542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082542 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(Br)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 84, 84, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 45, 10, 1, 1, 1, 1, 1, 84, 84] 84 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082542 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(Br)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 46, 46, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 12, 46, 84, 84, 84, 84, 84, 1, 1] 84 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082542 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082542 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082542/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082542 Building REAL300000082543 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082543' /scratch/stefan/7930160/working/building/REAL300000082543 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082543 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082543/0 /scratch/stefan/7930160/working/building/REAL300000082543 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/580 `/scratch/stefan/7930160/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2C(=C1)CCC(=O)N2C) `REAL300000082543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082543 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2C(=C1)CCC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 63, 170, 170, 170, 170, 170, 170, 170, 170, 170, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 170, 170, 170, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 170 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 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: REAL300000082543 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C2C(=C1)CCC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 170, 170, 51, 170, 170, 170, 170, 170, 170, 163, 170, 52, 52, 52, 10, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170] 170 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 463 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082543 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082543 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082543/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082543 Building REAL300000082544 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082544' /scratch/stefan/7930160/working/building/REAL300000082544 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082544 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082544/0 /scratch/stefan/7930160/working/building/REAL300000082544 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/581 `/scratch/stefan/7930160/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(F)=C23)=CC=C1F) `REAL300000082544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082544 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 30, 10, 1, 1, 1, 1, 1, 57, 57] 57 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 31]) 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: REAL300000082544 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 43, 43, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 11, 43, 57, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082544 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082544 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082544/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082544 Building REAL300000082545 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082545' /scratch/stefan/7930160/working/building/REAL300000082545 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082545 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082545/0 /scratch/stefan/7930160/working/building/REAL300000082545 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/582 `/scratch/stefan/7930160/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C(OC)C(OC)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082545 none CCC(CC1=CC=C(OC)C(OC)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 28, 6, 28, 53, 83, 83, 83, 83, 160, 83, 83, 159, 83, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 36, 36, 36, 36, 28, 53, 53, 83, 83, 160, 160, 160, 159, 159, 159, 83, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082545 none CCC(CC1=CC=C(OC)C(OC)=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 11, 2, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 11, 35, 35, 83, 83, 83, 83, 83, 83, 120, 120, 83, 14, 14, 14, 14, 14, 11, 2, 2, 1, 1, 4, 4, 4, 3, 3, 3, 1, 83, 83, 83] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 10, 11, 13, 35, 42] set([0, 1, 2, 9, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082545 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082545 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082545/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082545 Building REAL300000082546 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082546' /scratch/stefan/7930160/working/building/REAL300000082546 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082546 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082546/0 /scratch/stefan/7930160/working/building/REAL300000082546 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/583 `/scratch/stefan/7930160/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2N2CCCC2)=CC=C1F) `REAL300000082546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082546 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2N2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 58, 58, 58, 58, 58, 31, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 58, 58] 58 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082546 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2N2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 31, 31, 58, 58, 58, 49, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 8, 31, 58, 57, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1] 58 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082546 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2N2CCCC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 31, 10, 10, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 31, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58] 58 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082546 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082546 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082546/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082546 Building REAL300000082547 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082547' /scratch/stefan/7930160/working/building/REAL300000082547 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082547 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082547/0 /scratch/stefan/7930160/working/building/REAL300000082547 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/584 `/scratch/stefan/7930160/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082547 none CN(C)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 4, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 31, 36, 36, 36, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 6, 1, 1, 1] 36 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 88 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082547 none CN(C)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 4, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 1, 1, 1, 7, 20, 36, 36, 36] 36 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082547 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082547 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082547/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082547 Building REAL300000082548 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082548' /scratch/stefan/7930160/working/building/REAL300000082548 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082548 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082548/0 /scratch/stefan/7930160/working/building/REAL300000082548 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/585 `/scratch/stefan/7930160/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CC(F)(F)F)C2=CC=C(Cl)C=C2)=CC=C1F) `REAL300000082548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082548 none O=C([O-])C1=CC(NN=C(CC(F)(F)F)C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [132, 115, 132, 115, 115, 40, 6, 6, 1, 6, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 40, 18, 18, 1, 1, 1, 1, 115, 115] 137 rigid atoms, others: [32, 8, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 323 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: REAL300000082548 none O=C([O-])C1=CC(NN=C(CC(F)(F)F)C2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 47, 47, 107, 107, 107, 107, 47, 115, 115, 47, 60, 115, 115, 1, 1, 1, 1, 1, 11, 107, 107, 115, 115, 115, 115, 1, 1] 137 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 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]) total number of confs: 617 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082548 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082548 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082548/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082548 Building REAL300000082549 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082549' /scratch/stefan/7930160/working/building/REAL300000082549 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082549 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082549/0 /scratch/stefan/7930160/working/building/REAL300000082549 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/586 `/scratch/stefan/7930160/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082549 none CC(C)(C)OC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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 201 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, 159, 25, 159, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25] 201 rigid atoms, others: [40, 41, 42, 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, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082549 none CC(C)(C)OC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 26, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 40, 40, 25, 1, 1, 29, 29, 29, 28, 28, 28, 29, 29, 29, 1, 1, 1, 1, 1, 1, 25, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 44, 45, 46, 43, 23, 24, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082549 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082549 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082549/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082549 Building REAL300000082550 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082550' /scratch/stefan/7930160/working/building/REAL300000082550 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082550 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082550/0 /scratch/stefan/7930160/working/building/REAL300000082550 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/587 `/scratch/stefan/7930160/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F) `REAL300000082550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082550 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [104, 81, 104, 81, 81, 32, 6, 6, 1, 1, 1, 1, 1, 10, 10, 1, 1, 10, 10, 10, 1, 1, 81, 81, 81, 81, 81, 31, 6, 1, 10, 10, 10, 81, 81] 169 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300000082550 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 58, 58, 81, 81, 81, 169, 169, 81, 108, 169, 169, 169, 81, 81, 1, 1, 1, 1, 1, 11, 58, 81, 169, 169, 169, 1, 1] 169 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082550 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 169, 92, 28, 28, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 169, 169, 169, 169, 169, 92, 28, 10, 1, 1, 1, 169, 169] 169 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 333 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082550 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082550/1 /scratch/stefan/7930160/working/building/REAL300000082550 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/588 `/scratch/stefan/7930160/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F) `REAL300000082550.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082550 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 93, 135, 93, 93, 48, 48, 8, 1, 1, 1, 1, 1, 8, 8, 1, 4, 8, 8, 8, 1, 1, 93, 93, 93, 93, 93, 8, 8, 1, 8, 8, 8, 93, 93] 201 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082550 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 32, 93, 93, 93, 201, 201, 134, 173, 201, 201, 201, 93, 93, 1, 1, 1, 1, 1, 32, 32, 93, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082550 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 137, 137, 34, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 201, 201, 201, 201, 201, 34, 34, 8, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 350 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082550 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082550 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082550/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082550/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082550 Building REAL300000082551 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082551' /scratch/stefan/7930160/working/building/REAL300000082551 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082551 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082551/0 /scratch/stefan/7930160/working/building/REAL300000082551 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/589 `/scratch/stefan/7930160/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(O)=CC(O)=C1) `REAL300000082551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082551 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(O)=CC(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 33, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 67, 67, 67, 1, 2, 1, 2, 1] 268 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 30, 32]) total number of confs: 139 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: REAL300000082551 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(O)=CC(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [35, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 67, 67, 67, 45, 67, 67, 67, 36, 36, 36, 10, 1, 1, 1, 67, 134, 62, 134, 67] 268 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 481 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082551 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082551 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082551/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082551 Building REAL300000082552 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082552' /scratch/stefan/7930160/working/building/REAL300000082552 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082552 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082552/0 /scratch/stefan/7930160/working/building/REAL300000082552 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/590 `/scratch/stefan/7930160/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)S1) `REAL300000082552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082552 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 94, 94, 177, 177, 177, 177, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 177, 177, 177, 1] 177 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082552 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [63, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 177, 177, 177, 177, 177, 63, 63, 63, 63, 1, 1, 1, 177] 177 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 24, 25, 26] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082552 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082552 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082552/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082552 Building REAL300000082553 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082553' /scratch/stefan/7930160/working/building/REAL300000082553 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082553 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082553/0 /scratch/stefan/7930160/working/building/REAL300000082553 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/591 `/scratch/stefan/7930160/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2[O-])=CC=C1F) `REAL300000082553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082553 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 12, 4, 1, 1, 19, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082553 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 9, 15, 19, 19, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082553 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082553/1 /scratch/stefan/7930160/working/building/REAL300000082553 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/592 `/scratch/stefan/7930160/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2O)=CC=C1F) `REAL300000082553.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082553 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 28, 8, 1, 1, 2, 51, 51] 102 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 105 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: REAL300000082553 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(F)=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 39, 39, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 11, 39, 51, 51, 102, 1, 1] 102 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: 190 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082553 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082553 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082553/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082553/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082553 Building REAL300000082554 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082554' /scratch/stefan/7930160/working/building/REAL300000082554 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082554 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082554/0 /scratch/stefan/7930160/working/building/REAL300000082554 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/593 `/scratch/stefan/7930160/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@H+]3CC2=CC=CC=C2)=CC=C1F) `REAL300000082554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 46, 46, 46, 46, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 5, 7, 7, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 46, 46] 137 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 84 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 137, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 137, 137, 137, 137, 137, 137, 137, 1, 1] 137 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 26, 27, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 492 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 56, 56, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 137, 137] 137 rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 202 number of broken/clashed sets: 137 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082554 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082554/1 /scratch/stefan/7930160/working/building/REAL300000082554 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/594 `/scratch/stefan/7930160/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@@H+]3CC2=CC=CC=C2)=CC=C1F) `REAL300000082554.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 12, 19, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 5, 9, 9, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 12, 12] 39 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 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: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 39, 39, 28, 39, 39, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 39, 39, 28, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 26, 27, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082554 none O=C([O-])C1=CC(N=NC2C[C@H]3CC[C@@H](C2)[N@@H+]3CC2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 77 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082554 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082554 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082554/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082554/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082554 Building REAL300000082555 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082555' /scratch/stefan/7930160/working/building/REAL300000082555 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082555 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082555/0 /scratch/stefan/7930160/working/building/REAL300000082555 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/595 `/scratch/stefan/7930160/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082555 none CCSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 196, 126, 73, 126, 126, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 126, 126, 201, 201, 201, 201, 201, 126, 126, 34, 34, 34, 8, 1, 1, 1, 126, 126] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 550 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082555 none CCSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [16, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 54, 126, 126, 126, 126, 126, 126, 158, 158, 126, 1, 1, 16, 16, 16, 16, 16, 1, 1, 13, 13, 13, 54, 126, 126, 126, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 424 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082555 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082555 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082555/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082555 Building REAL300000082556 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082556' /scratch/stefan/7930160/working/building/REAL300000082556 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082556 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082556/0 /scratch/stefan/7930160/working/building/REAL300000082556 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/596 `/scratch/stefan/7930160/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Br)C=C32)=CC=C1F) `REAL300000082556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082556 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 53 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: REAL300000082556 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082556 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082556 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082556/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082556 Building REAL300000082557 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082557' /scratch/stefan/7930160/working/building/REAL300000082557 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082557 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082557/0 /scratch/stefan/7930160/working/building/REAL300000082557 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/597 `/scratch/stefan/7930160/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(Br)=C23)=CC=C1F) `REAL300000082557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082557 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(Br)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 10, 1, 1, 1, 1, 1, 1, 42, 42] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082557 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(Br)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 10, 42, 42, 42, 42, 42, 42, 1, 1] 42 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082557 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082557 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082557/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082557 Building REAL300000082558 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082558' /scratch/stefan/7930160/working/building/REAL300000082558 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082558 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082558/0 /scratch/stefan/7930160/working/building/REAL300000082558 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/598 `/scratch/stefan/7930160/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C) `REAL300000082558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082558 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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: [200, 177, 167, 64, 167, 64, 64, 64, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 64, 64, 64, 200, 201, 201, 201, 201, 64, 64, 64, 64, 64, 64, 1, 1, 1, 64, 64, 64, 64, 64, 64] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082558 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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: [56, 24, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 64, 64, 64, 64, 64, 64, 96, 96, 64, 1, 1, 1, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 64, 64, 64, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 39, 40, 21, 22, 23, 38, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 35, 36, 37, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082558 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082558 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082558/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082558 Building REAL300000082559 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082559' /scratch/stefan/7930160/working/building/REAL300000082559 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082559 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082559/0 /scratch/stefan/7930160/working/building/REAL300000082559 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/599 `/scratch/stefan/7930160/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CS2)=N1) `REAL300000082559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082559 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 99, 99, 201, 201, 201, 201, 99, 99, 99, 99, 99, 35, 9, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082559 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 45, 99, 99, 99, 99, 99, 99, 128, 128, 99, 1, 1, 13, 13, 13, 13, 1, 2, 2, 2, 1, 13, 45, 99, 99, 99, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082559 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 49, 49, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 49, 132, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082559 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082559 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082559/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082559 Building REAL300000082560 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082560' /scratch/stefan/7930160/working/building/REAL300000082560 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082560 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082560/0 /scratch/stefan/7930160/working/building/REAL300000082560 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/600 `/scratch/stefan/7930160/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=C3)C=C2)=CC=C1F) `REAL300000082560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082560 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 50, 73, 50, 50, 22, 4, 4, 1, 1, 1, 1, 1, 1, 12, 34, 34, 12, 34, 34, 1, 1, 50, 50, 50, 50, 50, 22, 4, 1, 1, 34, 34, 12, 34, 34, 1, 1, 50, 50] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082560 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 32, 32, 50, 50, 50, 50, 186, 201, 201, 186, 201, 201, 50, 50, 1, 1, 1, 1, 1, 9, 32, 50, 50, 201, 201, 186, 201, 201, 50, 50, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082560 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 144, 65, 65, 34, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34, 201, 201, 201, 201, 201, 144, 65, 34, 34, 1, 1, 1, 1, 1, 34, 34, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 488 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082560 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082560 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082560/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082560 Building REAL300000082561 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082561' /scratch/stefan/7930160/working/building/REAL300000082561 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082561 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082561/0 /scratch/stefan/7930160/working/building/REAL300000082561 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/601 `/scratch/stefan/7930160/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl) `REAL300000082561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082561 none COC1=CC(Cl)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 80, 79, 117, 117, 117, 60, 60, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 117, 117, 117, 163, 163, 163, 117, 60, 10, 1, 1, 1, 117] 163 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082561 none COC1=CC(Cl)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 117, 117, 117, 117, 117, 117, 163, 163, 117, 1, 1, 1, 4, 4, 4, 1, 8, 47, 117, 117, 117, 1] 163 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082561 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082561 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082561/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082561 Building REAL300000082562 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082562' /scratch/stefan/7930160/working/building/REAL300000082562 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082562 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082562/0 /scratch/stefan/7930160/working/building/REAL300000082562 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/602 `/scratch/stefan/7930160/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082562 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 22, 75, 75, 75, 75, 75, 75, 75, 75, 75, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 75, 75, 75, 4, 4, 4, 4] 75 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082562 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 1, 4, 4, 1, 1, 1, 1, 8, 8, 51, 51, 51, 51, 51, 51, 75, 75, 51, 1, 1, 2, 2, 2, 4, 4, 1, 4, 4, 1, 1, 1, 1, 1, 51, 51, 51, 1, 1, 1, 1] 75 rigid atoms, others: [0, 1, 2, 35, 36, 33, 8, 9, 10, 11, 44, 34, 43, 41, 23, 24, 42, 37] set([3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082562 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 75, 75, 51, 75, 75, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 51, 51, 51, 51, 75, 75, 51, 75, 75, 51, 51, 51, 51, 51, 1, 1, 1, 51, 51, 51, 51] 75 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082562 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082562 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082562/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082562 Building REAL300000082563 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082563' /scratch/stefan/7930160/working/building/REAL300000082563 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082563 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082563/0 /scratch/stefan/7930160/working/building/REAL300000082563 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/603 `/scratch/stefan/7930160/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2F)=CC=C1F) `REAL300000082563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082563 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 54, 55, 54, 54, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 32, 8, 1, 1, 1, 54, 54] 55 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082563 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 37, 37, 54, 54, 54, 42, 54, 54, 54, 1, 1, 1, 1, 1, 10, 37, 54, 42, 54, 1, 1] 55 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082563 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082563 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082563/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082563 Building REAL300000082564 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082564' /scratch/stefan/7930160/working/building/REAL300000082564 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082564 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082564/0 /scratch/stefan/7930160/working/building/REAL300000082564 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/604 `/scratch/stefan/7930160/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Cl)=CC=C1F) `REAL300000082564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082564 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 38, 8, 1, 1, 1, 71, 71] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082564 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 40, 40, 71, 71, 71, 47, 71, 71, 71, 1, 1, 1, 1, 1, 10, 40, 71, 47, 71, 1, 1] 71 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082564 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082564 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082564/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082564 Building REAL300000082565 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082565' /scratch/stefan/7930160/working/building/REAL300000082565 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082565 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082565/0 /scratch/stefan/7930160/working/building/REAL300000082565 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/605 `/scratch/stefan/7930160/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1) `REAL300000082565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082565 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [49, 46, 65, 65, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 65, 65, 65, 65, 65, 65, 65, 65, 41, 11, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082565 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 32, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 2, 2, 2, 1, 1, 8, 32, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082565 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082565 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082565/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082565 Building REAL300000082566 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082566' /scratch/stefan/7930160/working/building/REAL300000082566 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082566 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082566/0 /scratch/stefan/7930160/working/building/REAL300000082566 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/606 `/scratch/stefan/7930160/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Cl)=CC=C1F) `REAL300000082566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082566 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 42, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 79, 79, 79, 79, 79, 42, 10, 1, 1, 1, 79, 79] 79 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082566 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 40, 40, 79, 79, 79, 79, 79, 79, 40, 79, 79, 79, 1, 1, 1, 1, 1, 10, 40, 79, 49, 79, 1, 1] 79 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: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082566 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082566 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082566/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082566 Building REAL300000082567 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082567' /scratch/stefan/7930160/working/building/REAL300000082567 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082567 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082567/0 /scratch/stefan/7930160/working/building/REAL300000082567 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/607 `/scratch/stefan/7930160/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=CC=C1F) `REAL300000082567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082567 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 91, 135, 91, 91, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 11, 11, 11, 11, 11, 11, 1, 91, 91, 90, 90, 91, 42, 10, 1, 1, 1, 7, 7, 11, 11, 11, 11, 1, 91, 91] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 40, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 367 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: REAL300000082567 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 39, 39, 91, 91, 91, 91, 91, 136, 141, 201, 201, 201, 201, 201, 201, 91, 1, 1, 1, 1, 1, 9, 39, 91, 91, 91, 141, 141, 201, 201, 201, 201, 91, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 369 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082567 none O=C([O-])C1=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 114, 42, 42, 11, 11, 11, 11, 11, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 201, 201, 114, 42, 11, 11, 11, 4, 4, 1, 1, 1, 1, 11, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41, 42]) total number of confs: 420 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082567 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082567 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082567/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082567 Building REAL300000082568 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082568' /scratch/stefan/7930160/working/building/REAL300000082568 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082568 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082568/0 /scratch/stefan/7930160/working/building/REAL300000082568 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/608 `/scratch/stefan/7930160/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC=CCC2=CC=C(Cl)C=C2)=CC=C1F) `REAL300000082568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082568 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 113, 113, 22, 22, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 22, 22, 3, 3, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082568 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(Cl)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 53, 53, 163, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 53, 53, 163, 163, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082568 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082568 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082568/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082568 Building REAL300000082569 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082569' /scratch/stefan/7930160/working/building/REAL300000082569 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082569 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082569/0 /scratch/stefan/7930160/working/building/REAL300000082569 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/609 `/scratch/stefan/7930160/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082569 none CCC1=CN=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 126, 126, 126, 81, 126, 126, 48, 48, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 166, 166, 166, 166, 166, 126, 126, 126, 48, 48, 48, 11, 1, 1, 1] 166 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 557 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082569 none CCC1=CN=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 126, 126, 126, 126, 126, 126, 130, 130, 126, 6, 6, 6, 6, 6, 1, 1, 1, 9, 9, 9, 39, 126, 126, 126] 166 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 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]) total number of confs: 240 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082569 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082569 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082569/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082569 Building REAL300000082570 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082570' /scratch/stefan/7930160/working/building/REAL300000082570 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082570 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082570/0 /scratch/stefan/7930160/working/building/REAL300000082570 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/610 `/scratch/stefan/7930160/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C(=NC(C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082570 none CC1=NN2C(=NC(C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 7, 4, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 167, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 167, 167, 167, 167, 167, 167, 167, 64, 12, 1, 1, 1] 167 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082570 none CC1=NN2C(=NC(C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 7, 4, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 71, 167, 167, 167, 167, 167, 167, 167, 167, 167, 1, 2, 2, 2, 2, 2, 2, 12, 71, 167, 167, 167] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082570 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082570 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082570/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082570 Building REAL300000082571 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082571' /scratch/stefan/7930160/working/building/REAL300000082571 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082571 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082571/0 /scratch/stefan/7930160/working/building/REAL300000082571 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/611 `/scratch/stefan/7930160/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082571 none CC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 39, 70, 137, 201, 201, 165, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 39, 39, 70, 70, 201, 201, 166, 201, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 579 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: REAL300000082571 none CC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 48, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 48, 28, 28, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 424 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082571 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082571 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082571/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082571 Building REAL300000082572 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082572' /scratch/stefan/7930160/working/building/REAL300000082572 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082572 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082572/0 /scratch/stefan/7930160/working/building/REAL300000082572 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/612 `/scratch/stefan/7930160/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(C(F)(F)F)=C1) `REAL300000082572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082572 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 64, 195, 195, 195, 195, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 64, 195, 195, 195, 1, 1, 1] 195 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 339 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: REAL300000082572 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [58, 59, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 195, 195, 96, 152, 195, 195, 195, 195, 195, 195, 59, 59, 59, 11, 1, 1, 1, 195, 195, 195] 195 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 571 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082572 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082572 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082572/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082572 Building REAL300000082573 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082573' /scratch/stefan/7930160/working/building/REAL300000082573 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082573 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082573/0 /scratch/stefan/7930160/working/building/REAL300000082573 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/613 `/scratch/stefan/7930160/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(F)=C2)=CC=C1F) `REAL300000082573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082573 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 54, 75, 54, 54, 27, 6, 6, 1, 1, 1, 1, 1, 1, 12, 39, 38, 1, 1, 1, 54, 54, 54, 54, 54, 27, 6, 1, 1, 39, 1, 54, 54] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 19, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 29, 31]) 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: REAL300000082573 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 22, 22, 54, 54, 54, 54, 159, 201, 201, 54, 54, 54, 1, 1, 1, 1, 1, 7, 22, 54, 54, 201, 54, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082573 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082573 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082573/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082573 Building REAL300000082574 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082574' /scratch/stefan/7930160/working/building/REAL300000082574 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082574 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082574/0 /scratch/stefan/7930160/working/building/REAL300000082574 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/614 `/scratch/stefan/7930160/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1) `REAL300000082574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082574 none COC1=CC=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [132, 97, 97, 97, 97, 97, 97, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 97, 97, 97, 132, 132, 132, 97, 97, 53, 10, 1, 1, 1, 97, 98] 133 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) 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: REAL300000082574 none COC1=CC=C2OC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 45, 98, 98, 98, 98, 98, 98, 133, 133, 98, 1, 1, 1, 2, 2, 2, 1, 1, 8, 44, 98, 98, 97, 1, 1] 133 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082574 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082574 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082574/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082574 Building REAL300000082575 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082575' /scratch/stefan/7930160/working/building/REAL300000082575 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082575 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082575/0 /scratch/stefan/7930160/working/building/REAL300000082575 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/615 `/scratch/stefan/7930160/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082575 none CC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 1, 1, 1, 35] 35 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 59 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: REAL300000082575 none CC1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 38] set([34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082575 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082575 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082575/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082575 Building REAL300000082576 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082576' /scratch/stefan/7930160/working/building/REAL300000082576 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082576 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082576/0 /scratch/stefan/7930160/working/building/REAL300000082576 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/616 `/scratch/stefan/7930160/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2C=C1) `REAL300000082576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082576 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 31, 31] 31 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) 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: REAL300000082576 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 10, 31, 31, 31, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 32, 22, 23, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 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/7930160/working/building/REAL300000082576 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082576/1 /scratch/stefan/7930160/working/building/REAL300000082576 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/617 `/scratch/stefan/7930160/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=NNC2=C1) `REAL300000082576.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082576 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=NNC2=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 66, 66, 66, 66, 29, 7, 1, 1, 1, 66, 66] 66 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, 32, 33]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082576 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=NNC2=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 12, 12, 46, 66, 66, 65, 65, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 12, 46, 66, 66, 66, 1, 1] 66 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082576 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082576 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082576/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082576/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082576 Building REAL300000082577 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082577' /scratch/stefan/7930160/working/building/REAL300000082577 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082577 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082577/0 /scratch/stefan/7930160/working/building/REAL300000082577 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/618 `/scratch/stefan/7930160/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=CC3=CC=CC=C23)=CC=C1F) `REAL300000082577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082577 none O=C([O-])C1=CC(NN=CC2=CN=CC3=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 55, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 55, 12, 1, 1, 1, 1, 1, 1, 104, 104] 104 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000082577 none O=C([O-])C1=CC(NN=CC2=CN=CC3=CC=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 52, 52, 104, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 12, 52, 104, 104, 104, 104, 104, 104, 1, 1] 104 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 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/7930160/working/building/REAL300000082577 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082577 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082577/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082577 Building REAL300000082578 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082578' /scratch/stefan/7930160/working/building/REAL300000082578 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082578 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082578/0 /scratch/stefan/7930160/working/building/REAL300000082578 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/619 `/scratch/stefan/7930160/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082578 none CC(C)CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 100, 101, 55, 55, 55, 55, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 101, 101, 101, 101, 101, 101, 101, 100, 100, 55, 25, 9, 1, 1, 1] 101 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082578 none CC(C)CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 4, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 1, 1, 1, 1, 1, 1, 6, 6, 21, 55, 55, 55, 55, 55, 55, 62, 62, 55, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 6, 21, 55, 55, 55] 101 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082578 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082578 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082578/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082578 Building REAL300000082579 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082579' /scratch/stefan/7930160/working/building/REAL300000082579 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082579 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082579/0 /scratch/stefan/7930160/working/building/REAL300000082579 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/620 `/scratch/stefan/7930160/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=CC=C1F) `REAL300000082579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082579 none O=C([O-])C1=CC(NN=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 45, 33, 33, 14, 3, 3, 1, 1, 1, 1, 1, 1, 8, 42, 58, 58, 42, 58, 58, 1, 1, 33, 33, 33, 33, 33, 14, 3, 1, 1, 42, 42, 58, 58, 42, 58, 58, 1, 1, 33, 33] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 321 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: REAL300000082579 none O=C([O-])C1=CC(NN=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 23, 23, 33, 33, 23, 33, 120, 181, 201, 201, 181, 201, 201, 33, 33, 1, 1, 1, 1, 1, 9, 23, 33, 33, 181, 181, 201, 201, 181, 201, 201, 33, 33, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 635 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082579 none O=C([O-])C1=CC(NN=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 97, 97, 58, 38, 58, 58, 15, 3, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 146, 97, 58, 58, 3, 3, 1, 1, 1, 1, 1, 58, 58, 201, 201] 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, 40, 41, 42]) total number of confs: 538 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082579 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082579 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082579/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082579 Building REAL300000082580 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082580' /scratch/stefan/7930160/working/building/REAL300000082580 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082580 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082580/0 /scratch/stefan/7930160/working/building/REAL300000082580 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/621 `/scratch/stefan/7930160/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=CC=C1F) `REAL300000082580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082580 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 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, 138, 57, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 140, 140, 140, 140, 140, 57, 10, 1, 1, 1, 1, 1, 140, 140] 140 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082580 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 64, 64, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 13, 63, 140, 140, 140, 140, 140, 1, 1] 140 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082580 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082580 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082580/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082580 Building REAL300000082581 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082581' /scratch/stefan/7930160/working/building/REAL300000082581 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082581 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082581/0 /scratch/stefan/7930160/working/building/REAL300000082581 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/622 `/scratch/stefan/7930160/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082581 none CCOC(=O)C(F)(F)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 132, 132, 64, 132, 30, 64, 64, 30, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 30, 30] 201 rigid atoms, others: [39, 40, 41, 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, 42, 43]) total number of confs: 817 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082581 none CCOC(=O)C(F)(F)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 21, 6, 21, 1, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 30, 30, 30, 30, 30, 30, 46, 46, 30, 1, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 8, 9, 10, 11, 12, 13, 43, 42, 25, 37, 31] set([0, 1, 2, 3, 4, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082581 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082581 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082581/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082581 Building REAL300000082582 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082582' /scratch/stefan/7930160/working/building/REAL300000082582 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082582 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082582/0 /scratch/stefan/7930160/working/building/REAL300000082582 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/623 `/scratch/stefan/7930160/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1C=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1) `REAL300000082582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082582 none COC(=O)CN1C=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 110, 201, 44, 44, 44, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 201, 201, 201, 110, 110, 44, 15, 15, 15, 15, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082582 none COC(=O)CN1C=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 6, 38, 1, 1, 1, 1, 1, 7, 7, 29, 29, 44, 44, 44, 44, 44, 44, 63, 63, 44, 1, 1, 38, 38, 38, 6, 6, 1, 7, 7, 7, 7, 44, 44, 44] 201 rigid atoms, others: [4, 5, 6, 7, 8, 22, 23, 29] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082582 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082582 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082582/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082582 Building REAL300000082583 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082583' /scratch/stefan/7930160/working/building/REAL300000082583 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082583 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082583/0 /scratch/stefan/7930160/working/building/REAL300000082583 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/624 `/scratch/stefan/7930160/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=CC(C(F)(F)F)=C2)=CC=C1F) `REAL300000082583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082583 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 66, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 149, 149, 149, 149, 149, 66, 12, 1, 1, 1, 149, 149] 149 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082583 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 57, 57, 149, 149, 149, 149, 149, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 13, 57, 149, 149, 149, 1, 1] 149 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: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082583 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082583 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082583/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082583 Building REAL300000082584 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082584' /scratch/stefan/7930160/working/building/REAL300000082584 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082584 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082584/0 /scratch/stefan/7930160/working/building/REAL300000082584 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/625 `/scratch/stefan/7930160/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=CC=C1F) `REAL300000082584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082584 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 81, 106, 81, 81, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 81, 81, 81, 81, 81, 37, 7, 1, 1, 1, 12, 12, 12, 12, 1, 81, 81] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36, 37]) total number of confs: 264 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: REAL300000082584 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 36, 36, 81, 81, 81, 81, 81, 201, 201, 201, 201, 201, 81, 1, 1, 1, 1, 1, 8, 36, 81, 81, 81, 201, 201, 201, 201, 81, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082584 none O=C([O-])C1=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 149, 55, 55, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 149, 55, 12, 12, 12, 1, 1, 1, 1, 12, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 471 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082584 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082584 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082584/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082584 Building REAL300000082585 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082585' /scratch/stefan/7930160/working/building/REAL300000082585 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082585 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082585/0 /scratch/stefan/7930160/working/building/REAL300000082585 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/626 `/scratch/stefan/7930160/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=CC=C1F) `REAL300000082585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082585 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 95, 95, 95, 95, 95, 30, 5, 1, 1, 1, 95, 95] 95 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082585 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 64, 64, 95, 95, 64, 78, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 13, 64, 95, 95, 95, 1, 1] 95 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: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082585 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082585 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082585/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082585 Building REAL300000082586 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082586' /scratch/stefan/7930160/working/building/REAL300000082586 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082586 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082586/0 /scratch/stefan/7930160/working/building/REAL300000082586 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/627 `/scratch/stefan/7930160/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082586 none COC1=C(Br)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 64, 64, 64, 64, 64, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 64, 76, 76, 76, 64, 31, 9, 1, 1, 1] 76 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082586 none COC1=C(Br)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 41, 64, 64, 63, 63, 64, 64, 76, 76, 64, 1, 8, 8, 8, 1, 8, 41, 64, 64, 64] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 24] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082586 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082586 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082586/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082586 Building REAL300000082587 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082587' /scratch/stefan/7930160/working/building/REAL300000082587 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082587 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082587/0 /scratch/stefan/7930160/working/building/REAL300000082587 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/628 `/scratch/stefan/7930160/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082587 none CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [34, 9, 34, 54, 76, 76, 76, 76, 76, 112, 112, 138, 138, 138, 138, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 34, 54, 54, 76, 76, 76, 76, 76, 76, 76, 138, 138, 138, 138, 138, 138, 138, 138, 138, 1, 1, 1] 138 rigid atoms, others: [51, 49, 50, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 491 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: REAL300000082587 none CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [9, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 11, 11, 11, 9, 43, 43, 76, 76, 76, 76, 76, 76, 97, 97, 76, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 76, 76, 76] 138 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082587 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082587 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082587/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082587 Building REAL300000082588 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082588' /scratch/stefan/7930160/working/building/REAL300000082588 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082588 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082588/0 /scratch/stefan/7930160/working/building/REAL300000082588 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/629 `/scratch/stefan/7930160/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-]) `REAL300000082588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082588 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082588 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 37, 37, 37, 37, 37, 37, 37, 37, 33, 33, 33, 8, 1, 1, 1, 37, 37] 37 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082588 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082588/1 /scratch/stefan/7930160/working/building/REAL300000082588 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/630 `/scratch/stefan/7930160/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O) `REAL300000082588.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082588 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [11, 1, 11, 11, 61, 115, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 115, 115, 115, 1, 1, 2] 230 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 227 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: REAL300000082588 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 115, 115, 115, 105, 115, 115, 115, 115, 41, 41, 41, 8, 1, 1, 1, 115, 115, 230] 230 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 452 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082588 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082588 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082588/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082588/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082588 Building REAL300000082589 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082589' /scratch/stefan/7930160/working/building/REAL300000082589 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082589 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082589/0 /scratch/stefan/7930160/working/building/REAL300000082589 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/631 `/scratch/stefan/7930160/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=COC2=CC=CC=C12) `REAL300000082589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082589 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 64, 144, 144, 144, 144, 144, 144, 145, 145, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 144, 144, 144, 1, 1, 1, 1, 1] 145 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082589 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 144, 144, 144, 144, 144, 144, 144, 144, 45, 45, 45, 10, 1, 1, 1, 144, 144, 144, 144, 144] 145 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/7930160/working/building/REAL300000082589 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082589 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082589/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082589 Building REAL300000082590 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082590' /scratch/stefan/7930160/working/building/REAL300000082590 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082590 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082590/0 /scratch/stefan/7930160/working/building/REAL300000082590 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/632 `/scratch/stefan/7930160/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082590 none COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [141, 125, 125, 125, 87, 125, 188, 188, 188, 125, 125, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 141, 141, 141, 125, 188, 188, 188, 188, 125, 125, 33, 33, 33, 11, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 597 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082590 none COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 12, 12, 45, 125, 125, 125, 125, 125, 125, 142, 142, 125, 4, 4, 4, 1, 5, 5, 5, 5, 1, 1, 12, 12, 12, 45, 125, 125, 125] 201 rigid atoms, others: [1, 2, 3, 4, 5, 9, 10, 11, 12, 34, 35, 29] set([0, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 314 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082590 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082590 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082590/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082590 Building REAL300000082591 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082591' /scratch/stefan/7930160/working/building/REAL300000082591 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082591 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082591/0 /scratch/stefan/7930160/working/building/REAL300000082591 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/633 `/scratch/stefan/7930160/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082591 none CC(C)(C)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25] 25 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 61 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: REAL300000082591 none CC(C)(C)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 1, 1, 1, 1] 25 rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 9, 7, 44, 45, 46, 43, 21, 22, 36, 38, 39, 37] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 39 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082591 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082591 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082591/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082591 Building REAL300000082592 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082592' /scratch/stefan/7930160/working/building/REAL300000082592 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082592 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082592/0 /scratch/stefan/7930160/working/building/REAL300000082592 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/634 `/scratch/stefan/7930160/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2)=CC=C1F) `REAL300000082592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082592 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 110, 110, 24, 24, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 24, 24, 3, 3, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082592 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 53, 53, 160, 201, 201, 160, 201, 201, 201, 1, 1, 1, 1, 1, 53, 53, 160, 160, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082592 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082592 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082592/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082592 Building REAL300000082593 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082593' /scratch/stefan/7930160/working/building/REAL300000082593 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082593 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082593/0 /scratch/stefan/7930160/working/building/REAL300000082593 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/635 `/scratch/stefan/7930160/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC(C(F)(F)F)=C2)=CC=C1F) `REAL300000082593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082593 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 64, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 162, 162, 161, 161, 162, 64, 12, 1, 1, 1, 162, 162] 162 rigid atoms, others: [32, 8, 9, 10, 11, 12, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082593 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 55, 55, 162, 162, 162, 162, 162, 162, 55, 162, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 11, 55, 162, 55, 162, 1, 1] 162 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082593 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082593 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082593/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082593 Building REAL300000082594 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082594' /scratch/stefan/7930160/working/building/REAL300000082594 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082594 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082594/0 /scratch/stefan/7930160/working/building/REAL300000082594 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/636 `/scratch/stefan/7930160/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082594 none COC1=CC=C(Br)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 84, 84, 84, 84, 84, 84, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 84, 118, 118, 118, 84, 84, 41, 10, 1, 1, 1, 84] 118 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, 32, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082594 none COC1=CC=C(Br)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 84, 84, 84, 84, 84, 84, 88, 88, 84, 1, 3, 3, 3, 1, 1, 10, 50, 84, 84, 84, 1] 118 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082594 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082594 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082594/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082594 Building REAL300000082595 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082595' /scratch/stefan/7930160/working/building/REAL300000082595 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082595 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082595/0 /scratch/stefan/7930160/working/building/REAL300000082595 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/637 `/scratch/stefan/7930160/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1) `REAL300000082595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082595 none N#CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 62, 62, 62, 49, 11, 1, 1, 1, 62] 62 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082595 none N#CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 7, 31, 62, 62, 62, 1] 62 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082595 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082595 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082595/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082595 Building REAL300000082596 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082596' /scratch/stefan/7930160/working/building/REAL300000082596 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082596 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082596/0 /scratch/stefan/7930160/working/building/REAL300000082596 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/638 `/scratch/stefan/7930160/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=CC=C1F) `REAL300000082596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082596 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 30, 30] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 42 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: REAL300000082596 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 1, 1] 30 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 53 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082596 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082596 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082596/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082596 Building REAL300000082597 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082597' /scratch/stefan/7930160/working/building/REAL300000082597 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082597 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082597/0 /scratch/stefan/7930160/working/building/REAL300000082597 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/639 `/scratch/stefan/7930160/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=CC=C1F) `REAL300000082597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082597 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 33, 33] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 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: REAL300000082597 none O=C([O-])C1=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082597 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082597 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082597/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082597 Building REAL300000082598 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082598' /scratch/stefan/7930160/working/building/REAL300000082598 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082598 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082598/0 /scratch/stefan/7930160/working/building/REAL300000082598 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/640 `/scratch/stefan/7930160/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082598 none CN1CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 106, 106, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 50, 12, 1, 1, 1, 106, 106] 106 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082598 none CN1CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 106, 106, 105, 105, 106, 106, 106, 106, 106, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 50, 106, 106, 106, 1, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 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/7930160/working/building/REAL300000082598 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082598 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082598/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082598 Building REAL300000082599 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082599' /scratch/stefan/7930160/working/building/REAL300000082599 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082599 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082599/0 /scratch/stefan/7930160/working/building/REAL300000082599 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/641 `/scratch/stefan/7930160/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082599 none CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 47, 139, 29, 47, 47, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 201, 201, 201, 201, 201, 29, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29] 201 rigid atoms, others: [36, 37, 38, 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, 39, 40]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082599 none CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 15, 3, 15, 1, 3, 3, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 29, 29, 29, 44, 44, 29, 1, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 29, 29, 29, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 39, 8, 9, 10, 11, 12, 40, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082599 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082599 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082599/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082599 Building REAL300000082600 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082600' /scratch/stefan/7930160/working/building/REAL300000082600 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082600 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082600/0 /scratch/stefan/7930160/working/building/REAL300000082600 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/642 `/scratch/stefan/7930160/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082600 none CC1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 1, 1, 1, 36, 36, 36, 36] 36 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 61 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: REAL300000082600 none CC1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 36, 36, 36, 1, 1, 1, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 35, 36, 37, 38] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 31]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082600 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082600 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082600/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082600 Building REAL300000082601 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082601' /scratch/stefan/7930160/working/building/REAL300000082601 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082601 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082601/0 /scratch/stefan/7930160/working/building/REAL300000082601 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/643 `/scratch/stefan/7930160/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1) `REAL300000082601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082601 none O=C([O-])CN1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 56, 56, 56, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 67, 67, 56, 23, 23, 1, 1, 1] 67 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082601 none O=C([O-])CN1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [14, 6, 14, 1, 1, 1, 1, 1, 8, 42, 42, 56, 56, 56, 56, 56, 56, 64, 64, 56, 1, 1, 6, 6, 1, 8, 8, 56, 56, 56] 67 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, 29]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082601 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082601/1 /scratch/stefan/7930160/working/building/REAL300000082601 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/644 `/scratch/stefan/7930160/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=N1) `REAL300000082601.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082601 none O=C([O-])CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 36, 38, 20, 20, 20, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 20, 36, 36, 20, 18, 4, 1, 1, 1] 38 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 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: REAL300000082601 none O=C([O-])CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 1, 1, 1, 1, 1, 4, 4, 12, 20, 20, 20, 20, 20, 20, 26, 26, 20, 1, 1, 8, 8, 1, 4, 12, 20, 20, 20] 38 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, 29]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082601 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082601 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082601/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082601/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082601 Building REAL300000082602 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082602' /scratch/stefan/7930160/working/building/REAL300000082602 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082602 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082602/0 /scratch/stefan/7930160/working/building/REAL300000082602 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/645 `/scratch/stefan/7930160/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C1=CC=CC=C1) `REAL300000082602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082602 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 15, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 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: REAL300000082602 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 25, 25, 25, 1, 1, 1, 2, 2, 1, 2, 2] 25 rigid atoms, others: [0, 1, 2, 3, 4, 34, 16, 17, 18, 35, 36, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082602 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 25, 25, 2, 2, 2, 1, 1, 1, 1, 1] 25 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 34 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082602 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082602 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082602/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082602 Building REAL300000082603 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082603' /scratch/stefan/7930160/working/building/REAL300000082603 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082603 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082603/0 /scratch/stefan/7930160/working/building/REAL300000082603 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/646 `/scratch/stefan/7930160/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1) `REAL300000082603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082603 none COC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 128, 128, 128, 128, 128, 80, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 54, 54, 128, 181, 181, 181, 128, 128, 128, 80, 80, 34, 1, 1, 1, 54, 54, 54, 54, 54, 128] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082603 none COC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 11, 63, 63, 128, 128, 128, 128, 128, 128, 182, 182, 128, 11, 27, 27, 1, 3, 3, 3, 1, 1, 1, 2, 2, 11, 128, 128, 128, 27, 27, 27, 27, 27, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082603 none COC1=CC=CC(CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 15, 5, 1, 5, 23, 23, 54, 54, 54, 54, 54, 54, 83, 83, 54, 1, 1, 1, 27, 39, 39, 39, 27, 27, 27, 15, 15, 5, 54, 54, 54, 1, 1, 1, 1, 1, 27] 201 rigid atoms, others: [37, 38, 39, 8, 41, 40, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082603 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082603 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082603/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082603 Building REAL300000082604 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082604' /scratch/stefan/7930160/working/building/REAL300000082604 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082604 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082604/0 /scratch/stefan/7930160/working/building/REAL300000082604 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/647 `/scratch/stefan/7930160/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)O1) `REAL300000082604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082604 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 12, 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, 7, 4, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 37, 61, 61, 61, 61, 61, 61, 72, 72, 61, 1, 11, 11, 11, 11, 11, 11, 1, 7, 37, 61, 61, 61] 98 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 29] set([0, 1, 2, 3, 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: 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: REAL300000082604 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 12, 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, 7, 4, 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 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, 11, 11, 11, 11, 35, 35, 87, 98, 98, 98, 98, 98, 98, 98, 98, 98, 11, 1, 2, 2, 2, 1, 1, 11, 35, 87, 98, 98, 98] 98 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082604 none CC1=CC=C(C2=NC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 12, 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, 7, 4, 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 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, 61, 61, 61, 61, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 98, 98, 98, 98, 98, 98, 61, 23, 5, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082604 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082604 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082604/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082604 Building REAL300000082605 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082605' /scratch/stefan/7930160/working/building/REAL300000082605 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082605 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082605/0 /scratch/stefan/7930160/working/building/REAL300000082605 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/648 `/scratch/stefan/7930160/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CO)C2=CC=C(F)C=C2F)=CC=C1F) `REAL300000082605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082605 none O=C([O-])C1=CC(NN=C(CO)C2=CC=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [137, 109, 137, 109, 109, 41, 12, 12, 1, 12, 32, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 41, 32, 32, 96, 1, 1, 1, 109, 109] 423 rigid atoms, others: [8, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 31]) total number of confs: 476 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: REAL300000082605 none O=C([O-])C1=CC(NN=C(CO)C2=CC=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 49, 49, 108, 49, 109, 109, 55, 109, 109, 109, 109, 1, 1, 1, 1, 1, 10, 108, 108, 324, 109, 109, 109, 1, 1] 423 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 930 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082605 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082605 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082605/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082605 Building REAL300000082606 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082606' /scratch/stefan/7930160/working/building/REAL300000082606 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082606 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082606/0 /scratch/stefan/7930160/working/building/REAL300000082606 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/649 `/scratch/stefan/7930160/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1) `REAL300000082606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082606 none CC(C)(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 9, 9, 26, 104, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 3, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 26, 26, 201, 201, 201, 2, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 16, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 370 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: REAL300000082606 none CC(C)(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 41, 130, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 130, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 137, 41, 41, 1, 1, 1, 194, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 15, 37] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 961 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082606 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082606 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082606/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082606 Building REAL300000082607 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082607' /scratch/stefan/7930160/working/building/REAL300000082607 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082607 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082607/0 /scratch/stefan/7930160/working/building/REAL300000082607 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/650 `/scratch/stefan/7930160/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1) `REAL300000082607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082607 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 56, 12, 1, 1, 1, 161, 161, 161, 161] 161 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082607 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 70, 161, 161, 161, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 70, 161, 161, 161, 1, 1, 1, 1] 161 rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082607 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082607 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082607/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082607 Building REAL300000082608 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082608' /scratch/stefan/7930160/working/building/REAL300000082608 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082608 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082608/0 /scratch/stefan/7930160/working/building/REAL300000082608 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/651 `/scratch/stefan/7930160/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1) `REAL300000082608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082608 none COC1=CC=C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29, 29] 50 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082608 none COC1=CC=C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 29, 50, 50, 29, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 1, 1, 1] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39] set([0, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082608 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082608 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082608/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082608 Building REAL300000082609 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082609' /scratch/stefan/7930160/working/building/REAL300000082609 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082609 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082609/0 /scratch/stefan/7930160/working/building/REAL300000082609 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/652 `/scratch/stefan/7930160/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=CC=C1F) `REAL300000082609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082609 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 83, 102, 83, 83, 34, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 83, 83, 82, 82, 83, 34, 8, 1, 1, 3, 3, 3, 3, 1, 83, 83] 102 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082609 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 58, 58, 83, 83, 67, 83, 102, 102, 83, 102, 102, 83, 83, 83, 1, 1, 1, 1, 1, 13, 58, 83, 83, 102, 102, 102, 102, 83, 1, 1] 102 rigid atoms, others: [1, 3, 4, 5, 6, 25, 22, 23, 24, 36, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082609 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 52, 15, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 102, 102, 102, 102, 102, 52, 15, 3, 3, 1, 1, 1, 1, 3, 102, 102] 102 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082609 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082609 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082609/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082609 Building REAL300000082610 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082610' /scratch/stefan/7930160/working/building/REAL300000082610 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082610 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082610/0 /scratch/stefan/7930160/working/building/REAL300000082610 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/653 `/scratch/stefan/7930160/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=CC=C1F) `REAL300000082610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082610 none O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082610 none O=C([O-])C1=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 9, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082610 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082610 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082610/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082610 Building REAL300000082611 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082611' /scratch/stefan/7930160/working/building/REAL300000082611 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082611 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082611/0 /scratch/stefan/7930160/working/building/REAL300000082611 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/654 `/scratch/stefan/7930160/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1) `REAL300000082611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082611 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 46, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 46, 84, 84, 84, 1, 1, 1] 84 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000082611 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 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: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 84, 84, 24, 24, 84, 84, 84, 84, 84, 24, 24, 24, 6, 1, 1, 1, 84, 84, 84] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082611 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082611 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082611/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082611 Building REAL300000082612 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082612' /scratch/stefan/7930160/working/building/REAL300000082612 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082612 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082612/0 /scratch/stefan/7930160/working/building/REAL300000082612 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/655 `/scratch/stefan/7930160/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=CC=C1F) `REAL300000082612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082612 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens 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, 68, 104, 68, 68, 32, 7, 7, 1, 1, 1, 1, 1, 1, 13, 35, 35, 21, 35, 35, 1, 68, 68, 68, 68, 68, 32, 7, 1, 1, 35, 35, 35, 35, 35, 68, 68] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082612 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 39, 39, 68, 68, 68, 68, 173, 201, 201, 190, 201, 201, 68, 1, 1, 1, 1, 1, 9, 39, 68, 68, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082612 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 158, 71, 71, 35, 35, 35, 35, 5, 1, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 201, 158, 71, 35, 35, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 464 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082612 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082612 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082612/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082612 Building REAL300000082613 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082613' /scratch/stefan/7930160/working/building/REAL300000082613 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082613 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082613/0 /scratch/stefan/7930160/working/building/REAL300000082613 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/656 `/scratch/stefan/7930160/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F) `REAL300000082613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [106, 86, 106, 86, 86, 35, 7, 7, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 7, 6, 1, 1, 86, 86, 86, 86, 86, 35, 7, 1, 7, 7, 7, 86, 86] 146 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 56, 56, 86, 86, 86, 146, 146, 126, 146, 146, 146, 146, 86, 86, 1, 1, 1, 1, 1, 11, 56, 85, 146, 146, 145, 1, 1] 146 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 78, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 146, 146, 146, 146, 146, 78, 21, 7, 1, 1, 1, 146, 146] 146 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082613 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082613/1 /scratch/stefan/7930160/working/building/REAL300000082613 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/657 `/scratch/stefan/7930160/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F) `REAL300000082613.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 118, 101, 101, 53, 53, 9, 1, 1, 1, 1, 1, 7, 7, 2, 6, 7, 7, 7, 1, 1, 101, 101, 101, 101, 101, 9, 9, 1, 7, 7, 7, 101, 101] 201 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 33, 101, 101, 101, 201, 201, 178, 201, 201, 201, 201, 101, 101, 1, 1, 1, 1, 1, 33, 33, 101, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082613 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 121, 121, 29, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 29, 29, 7, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 351 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082613 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082613 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082613/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082613/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082613 Building REAL300000082614 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082614' /scratch/stefan/7930160/working/building/REAL300000082614 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082614 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082614/0 /scratch/stefan/7930160/working/building/REAL300000082614 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/658 `/scratch/stefan/7930160/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F) `REAL300000082614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082614 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [107, 87, 107, 87, 87, 36, 7, 7, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 1, 1, 87, 87, 87, 87, 87, 36, 7, 1, 6, 6, 6, 87, 87] 147 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300000082614 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 56, 56, 87, 87, 87, 147, 147, 127, 147, 147, 147, 147, 87, 87, 1, 1, 1, 1, 1, 11, 56, 86, 147, 147, 147, 1, 1] 147 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082614 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 79, 21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 147, 147, 147, 147, 147, 79, 21, 6, 1, 1, 1, 147, 147] 147 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082614 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082614/1 /scratch/stefan/7930160/working/building/REAL300000082614 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/659 `/scratch/stefan/7930160/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F) `REAL300000082614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082614 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 102, 118, 102, 102, 53, 53, 9, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 1, 1, 102, 102, 102, 102, 102, 9, 9, 1, 7, 7, 7, 102, 102] 201 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082614 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 33, 102, 102, 102, 201, 201, 198, 201, 201, 201, 201, 102, 102, 1, 1, 1, 1, 1, 33, 33, 102, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082614 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 27, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 27, 27, 7, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082614 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082614 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082614/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082614/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082614 Building REAL300000082615 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082615' /scratch/stefan/7930160/working/building/REAL300000082615 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082615 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082615/0 /scratch/stefan/7930160/working/building/REAL300000082615 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/660 `/scratch/stefan/7930160/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082615 none CC(C)(C)C1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 139, 148, 148, 129, 139, 139, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 139, 139, 148, 148, 148, 148, 148, 148, 148, 148, 148, 139, 139, 139, 139, 139, 139, 57, 58, 1, 1, 1, 139, 139, 139, 139] 148 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082615 none CC(C)(C)C1CCC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 53, 53, 139, 139, 139, 139, 139, 139, 148, 148, 139, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 139, 139, 139, 1, 1, 1, 1] 148 rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 21, 22, 36, 37] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 255 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082615 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082615 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082615/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082615 Building REAL300000082616 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082616' /scratch/stefan/7930160/working/building/REAL300000082616 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082616 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082616/0 /scratch/stefan/7930160/working/building/REAL300000082616 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/661 `/scratch/stefan/7930160/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=CC=C1F) `REAL300000082616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082616 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [125, 85, 125, 85, 85, 32, 8, 8, 1, 1, 1, 1, 1, 1, 2, 10, 20, 20, 10, 20, 20, 1, 1, 1, 85, 85, 85, 85, 85, 32, 8, 1, 1, 10, 10, 21, 21, 20, 21, 21, 1, 2, 85, 85] 402 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 40, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 396 number of broken/clashed sets: 175 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082616 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 54, 54, 85, 85, 85, 85, 130, 153, 201, 201, 173, 201, 201, 85, 85, 85, 1, 1, 1, 1, 1, 11, 54, 85, 85, 153, 153, 201, 201, 201, 201, 201, 85, 170, 1, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 733 number of broken/clashed sets: 175 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082616 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 111, 48, 48, 20, 20, 20, 20, 11, 3, 1, 1, 1, 1, 1, 1, 1, 20, 20, 21, 201, 201, 201, 201, 201, 111, 48, 21, 20, 3, 3, 1, 1, 1, 1, 1, 21, 41, 201, 201] 402 rigid atoms, others: [35, 36, 37, 38, 39, 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, 40, 41, 42, 43]) total number of confs: 461 number of broken/clashed sets: 175 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082616 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082616 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082616/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082616 Building REAL300000082617 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082617' /scratch/stefan/7930160/working/building/REAL300000082617 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082617 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082617/0 /scratch/stefan/7930160/working/building/REAL300000082617 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/662 `/scratch/stefan/7930160/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=CC=C1F) `REAL300000082617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082617 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 36, 9, 1, 1, 1, 75, 75] 75 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082617 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 49, 49, 75, 75, 49, 59, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 13, 49, 75, 75, 75, 1, 1] 75 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082617 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082617 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082617/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082617 Building REAL300000082618 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082618' /scratch/stefan/7930160/working/building/REAL300000082618 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082618 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082618/0 /scratch/stefan/7930160/working/building/REAL300000082618 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/663 `/scratch/stefan/7930160/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])S2)=CC=C1F) `REAL300000082618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082618 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'S.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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 108, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 107, 46, 8, 1, 1, 108, 108] 108 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082618 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'S.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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 62, 62, 107, 107, 107, 108, 107, 108, 108, 1, 1, 1, 1, 1, 12, 62, 107, 107, 1, 1] 108 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082618 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082618 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082618/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082618 Building REAL300000082619 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082619' /scratch/stefan/7930160/working/building/REAL300000082619 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082619 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082619/0 /scratch/stefan/7930160/working/building/REAL300000082619 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/664 `/scratch/stefan/7930160/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082619 none CC(C)CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 134, 146, 69, 69, 69, 32, 32, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 146, 146, 146, 146, 146, 146, 146, 134, 134, 69, 32, 11, 1, 1, 1, 69] 146 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082619 none CC(C)CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 6, 6, 26, 69, 69, 68, 68, 69, 69, 95, 95, 69, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 6, 26, 69, 69, 69, 1] 146 rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 37, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082619 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082619 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082619/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082619 Building REAL300000082620 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082620' /scratch/stefan/7930160/working/building/REAL300000082620 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082620 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082620/0 /scratch/stefan/7930160/working/building/REAL300000082620 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/665 `/scratch/stefan/7930160/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082620 none CCC1=CC=CN=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 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, 114, 114, 114, 114, 114, 114, 50, 50, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 150, 150, 150, 150, 150, 114, 114, 114, 50, 50, 50, 11, 1, 1, 1] 150 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 400 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082620 none CCC1=CC=CN=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 36, 114, 114, 114, 114, 114, 114, 124, 124, 114, 6, 6, 6, 6, 6, 1, 1, 1, 8, 8, 8, 36, 114, 114, 114] 150 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 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]) total number of confs: 248 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082620 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082620/1 /scratch/stefan/7930160/working/building/REAL300000082620 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/666 `/scratch/stefan/7930160/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082620 none CCC1=CC=CN=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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, 93, 93, 93, 93, 93, 93, 49, 9, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 131, 131, 131, 131, 131, 93, 93, 93, 49, 49, 49, 49, 1, 1, 1] 131 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 452 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082620 none CCC1=CC=CN=C1C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 93, 93, 93, 93, 93, 93, 105, 105, 93, 6, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 93, 93, 93] 131 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 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]) total number of confs: 200 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082620 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082620 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082620/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082620/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082620 Building REAL300000082621 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082621' /scratch/stefan/7930160/working/building/REAL300000082621 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082621 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082621/0 /scratch/stefan/7930160/working/building/REAL300000082621 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/667 `/scratch/stefan/7930160/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2CCCCC2)=N1) `REAL300000082621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082621 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 117, 117, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 117, 118, 170, 170, 170, 170, 170, 117, 118, 118, 118, 118, 38, 8, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170] 170 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300000082621 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 61, 118, 118, 118, 118, 118, 118, 137, 137, 118, 1, 1, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 12, 60, 118, 118, 117, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 170 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 318 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082621 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 37, 37, 123, 170, 170, 170, 170, 170, 170, 170, 170, 169, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 37, 123, 170, 170, 169, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 170 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 387 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082621 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082621 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082621/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082621 Building REAL300000082622 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082622' /scratch/stefan/7930160/working/building/REAL300000082622 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082622 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082622/0 /scratch/stefan/7930160/working/building/REAL300000082622 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/668 `/scratch/stefan/7930160/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082622 none COCCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 196, 159, 69, 69, 69, 69, 69, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 201, 201, 201, 196, 196, 159, 159, 69, 69, 69, 23, 23, 23, 4, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37]) total number of confs: 727 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082622 none COCCC1=NC(C)=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [28, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 69, 69, 69, 69, 69, 69, 97, 97, 69, 1, 28, 28, 28, 12, 12, 8, 8, 2, 2, 2, 8, 8, 8, 33, 69, 69, 69] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 326 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082622 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082622 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082622/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082622 Building REAL300000082623 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082623' /scratch/stefan/7930160/working/building/REAL300000082623 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082623 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082623/0 /scratch/stefan/7930160/working/building/REAL300000082623 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/669 `/scratch/stefan/7930160/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=CC=C(Cl)C=C32)=CC=C1F) `REAL300000082623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082623 none O=C([O-])C1=CC(NN=C2CCOC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 41, 41] 41 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 61 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: REAL300000082623 none O=C([O-])C1=CC(NN=C2CCOC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 11, 41, 41, 41, 41, 41, 41, 41, 1, 1] 41 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082623 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082623 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082623/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082623 Building REAL300000082624 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082624' /scratch/stefan/7930160/working/building/REAL300000082624 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082624 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082624/0 /scratch/stefan/7930160/working/building/REAL300000082624 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/670 `/scratch/stefan/7930160/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC(F)=C23)=CC=C1F) `REAL300000082624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082624 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 9, 1, 1, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 56 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: REAL300000082624 none O=C([O-])C1=CC(NN=C2CCOC3=C(F)C=CC(F)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 9, 38, 38, 38, 38, 38, 38, 1, 1] 38 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082624 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082624 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082624/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082624 Building REAL300000082625 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082625' /scratch/stefan/7930160/working/building/REAL300000082625 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082625 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082625/0 /scratch/stefan/7930160/working/building/REAL300000082625 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/671 `/scratch/stefan/7930160/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=C2C=C(F)C=C3[N+](=O)[O-])=CC=C1F) `REAL300000082625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082625 none O=C([O-])C1=CC(NN=C2CCOC3=C2C=C(F)C=C3[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 54, 55, 54, 54, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 54, 54, 54, 54, 54, 9, 1, 1, 1, 1, 1, 1, 54, 54] 55 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 80 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: REAL300000082625 none O=C([O-])C1=CC(NN=C2CCOC3=C2C=C(F)C=C3[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 55, 55, 1, 1, 1, 1, 1, 10, 54, 54, 54, 54, 54, 54, 1, 1] 55 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082625 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082625 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082625/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082625 Building REAL300000082626 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082626' /scratch/stefan/7930160/working/building/REAL300000082626 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082626 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082626/0 /scratch/stefan/7930160/working/building/REAL300000082626 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/672 `/scratch/stefan/7930160/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082626 none CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 109, 42, 109, 42, 42, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 42, 201, 201, 201, 201, 201, 201, 201, 201, 201, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [42, 43, 44, 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, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082626 none CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 42, 42, 42, 42, 42, 42, 70, 70, 42, 1, 1, 22, 22, 22, 21, 21, 21, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 45, 46, 47, 48, 40, 41, 24, 25, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082626 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082626 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082626/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082626 Building REAL300000082627 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082627' /scratch/stefan/7930160/working/building/REAL300000082627 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082627 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082627/0 /scratch/stefan/7930160/working/building/REAL300000082627 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/673 `/scratch/stefan/7930160/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl) `REAL300000082627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082627 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 40, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 40, 102, 102, 102, 1, 1, 1] 102 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000082627 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 102, 102, 74, 76, 102, 102, 102, 102, 102, 54, 54, 54, 11, 1, 1, 1, 102, 102, 102] 102 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/7930160/working/building/REAL300000082627 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082627 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082627/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082627 Building REAL300000082628 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082628' /scratch/stefan/7930160/working/building/REAL300000082628 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082628 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082628/0 /scratch/stefan/7930160/working/building/REAL300000082628 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/674 `/scratch/stefan/7930160/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC3C[N@H+](CC4=CC=CC=C4)CC32)=CC=C1F) `REAL300000082628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 42, 57, 42, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 7, 9, 9, 1, 1, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 7, 9, 9, 1, 1, 1, 42, 42] 87 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 50, 51]) total number of confs: 143 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: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 82, 87, 87, 84, 87, 87, 42, 42, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 82, 82, 87, 87, 84, 87, 87, 42, 42, 42, 1, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 50, 51, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 306 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 52, 52, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 87, 87, 87, 87, 87, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 87, 87] 87 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082628 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082628/1 /scratch/stefan/7930160/working/building/REAL300000082628 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/675 `/scratch/stefan/7930160/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC3C[N@@H+](CC4=CC=CC=C4)CC32)=CC=C1F) `REAL300000082628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 42, 56, 42, 42, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 1, 1, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 42, 42] 87 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 50, 51]) total number of confs: 133 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: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 42, 42, 42, 42, 42, 42, 42, 42, 82, 87, 87, 87, 87, 87, 42, 42, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 82, 82, 87, 87, 87, 87, 87, 42, 42, 42, 1, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 50, 51, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 296 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082628 none O=C([O-])C1=CC(N=NC2CCCC3C[N@@H+](CC4=CC=CC=C4)CC32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 51, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 87, 87, 87, 87, 87, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 87, 87] 87 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082628 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082628 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082628/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082628/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082628 Building REAL300000082629 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082629' /scratch/stefan/7930160/working/building/REAL300000082629 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082629 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082629/0 /scratch/stefan/7930160/working/building/REAL300000082629 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/676 `/scratch/stefan/7930160/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=CC=C1F) `REAL300000082629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082629 none O=C([O-])C1=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 42, 68, 42, 42, 16, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 42, 42, 41, 41, 42, 16, 6, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 42, 42] 131 rigid atoms, others: [8, 9, 10, 11, 12, 13, 47, 23, 31] 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) 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: REAL300000082629 none O=C([O-])C1=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 37, 37, 42, 42, 42, 42, 131, 131, 131, 131, 131, 131, 131, 131, 131, 42, 1, 1, 1, 1, 1, 11, 37, 42, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 42, 1, 1] 131 rigid atoms, others: [1, 3, 4, 5, 6, 48, 49, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082629 none O=C([O-])C1=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 19, 19, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 131, 131, 131, 131, 131, 47, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 131, 131] 131 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082629 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082629 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082629/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082629 Building REAL300000082630 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082630' /scratch/stefan/7930160/working/building/REAL300000082630 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082630 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082630/0 /scratch/stefan/7930160/working/building/REAL300000082630 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/677 `/scratch/stefan/7930160/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C(Br)C=CC=C23)=CC=C1F) `REAL300000082630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082630 none O=C([O-])C1=CC(NN=C2CCCC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 55 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: REAL300000082630 none O=C([O-])C1=CC(NN=C2CCCC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082630 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082630 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082630/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082630 Building REAL300000082631 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082631' /scratch/stefan/7930160/working/building/REAL300000082631 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082631 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082631/0 /scratch/stefan/7930160/working/building/REAL300000082631 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/678 `/scratch/stefan/7930160/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(F)=C3)C2)=CC=C1F) `REAL300000082631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082631 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(F)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [81, 54, 81, 54, 54, 13, 13, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 1, 54, 54, 54, 54, 54, 1, 1, 1, 1, 13, 13, 12, 13, 1, 1, 54, 54] 162 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 28, 29, 30, 31, 34, 35]) total number of confs: 191 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: REAL300000082631 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(F)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 54, 54, 54, 162, 162, 162, 162, 162, 162, 54, 1, 1, 1, 1, 1, 54, 54, 54, 54, 162, 162, 162, 162, 54, 54, 1, 1] 162 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 267 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082631 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(F)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 78, 78, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 162, 162, 162, 162, 162, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 162, 162] 162 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 237 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082631 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082631 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082631/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082631 Building REAL300000082632 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082632' /scratch/stefan/7930160/working/building/REAL300000082632 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082632 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082632/0 /scratch/stefan/7930160/working/building/REAL300000082632 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/679 `/scratch/stefan/7930160/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082632 none CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 114, 122, 122, 114, 114, 91, 91, 91, 91, 91, 91, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 122, 122, 122, 122, 122, 122, 122, 122, 122, 114, 91, 91, 91, 39, 9, 1, 1, 1] 122 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000082632 none CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 49, 91, 91, 91, 91, 91, 91, 103, 103, 91, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 11, 49, 91, 91, 91] 122 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082632 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082632 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082632/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082632 Building REAL300000082633 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082633' /scratch/stefan/7930160/working/building/REAL300000082633 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082633 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082633/0 /scratch/stefan/7930160/working/building/REAL300000082633 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/680 `/scratch/stefan/7930160/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=C1) `REAL300000082633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082633 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 16, 17, 17, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 54, 54, 54, 54, 54, 54, 77, 77, 54, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 24, 54, 54, 54, 1, 1, 17, 17] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 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: REAL300000082633 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 57, 57, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 17, 1, 1, 2, 2, 2, 1, 1, 17, 17, 57, 109, 201, 201, 201, 17, 17, 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: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082633 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 130, 54, 32, 54, 54, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 54, 54, 17, 5, 1, 1, 1, 54, 54, 201, 201] 201 rigid atoms, others: [37, 38, 39, 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, 40, 41, 42, 43]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082633 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082633 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082633/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082633 Building REAL300000082634 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082634' /scratch/stefan/7930160/working/building/REAL300000082634 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082634 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082634/0 /scratch/stefan/7930160/working/building/REAL300000082634 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/681 `/scratch/stefan/7930160/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1) `REAL300000082634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082634 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 12, 12, 75, 152, 152, 152, 152, 152, 152, 176, 176, 152, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 75, 152, 152, 152, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 488 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: REAL300000082634 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 152, 152, 152, 139, 152, 152, 152, 50, 50, 50, 50, 50, 6, 1, 1, 1, 152, 152, 152] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 389 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082634 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082634 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082634/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082634 Building REAL300000082635 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082635' /scratch/stefan/7930160/working/building/REAL300000082635 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082635 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082635/0 /scratch/stefan/7930160/working/building/REAL300000082635 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/682 `/scratch/stefan/7930160/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC=C(F)C=C32)=CC=C1F) `REAL300000082635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082635 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 53 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: REAL300000082635 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(F)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082635 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082635 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082635/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082635 Building REAL300000082636 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082636' /scratch/stefan/7930160/working/building/REAL300000082636 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082636 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082636/0 /scratch/stefan/7930160/working/building/REAL300000082636 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/683 `/scratch/stefan/7930160/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=CC=C1F) `REAL300000082636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082636 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 59, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 125, 125, 126, 59, 10, 1, 1, 1, 126, 126] 126 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082636 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 55, 55, 126, 126, 94, 126, 126, 126, 126, 1, 1, 1, 1, 1, 13, 55, 126, 126, 126, 1, 1] 126 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: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082636 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082636 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082636/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082636 Building REAL300000082637 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082637' /scratch/stefan/7930160/working/building/REAL300000082637 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082637 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082637/0 /scratch/stefan/7930160/working/building/REAL300000082637 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/684 `/scratch/stefan/7930160/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=CC=C1F) `REAL300000082637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082637 none O=C([O-])C1=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 47, 43, 43, 13, 13, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 1, 1, 43, 43, 43, 43, 43, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 43, 43] 49 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30, 31, 32, 33, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082637 none O=C([O-])C1=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 49, 49, 43, 48, 49, 49, 43, 43, 1, 1, 1, 1, 1, 43, 43, 43, 43, 49, 49, 49, 49, 43, 43, 43, 43, 1, 1] 49 rigid atoms, others: [1, 3, 4, 5, 6, 39, 21, 22, 23, 24, 25, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082637 none O=C([O-])C1=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 30, 30, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 49, 49, 49, 49, 49, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 49, 49] 49 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082637 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082637 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082637/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082637 Building REAL300000082638 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082638' /scratch/stefan/7930160/working/building/REAL300000082638 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082638 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082638/0 /scratch/stefan/7930160/working/building/REAL300000082638 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/685 `/scratch/stefan/7930160/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1) `REAL300000082638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082638 none COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 97, 62, 131, 131, 62, 62, 62, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 131, 131, 131, 201, 201, 201, 131, 131, 62, 62, 62, 13, 1, 1, 1, 131] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 583 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082638 none COC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 131, 131, 131, 131, 131, 131, 201, 201, 131, 1, 1, 1, 3, 3, 3, 1, 1, 8, 8, 8, 38, 131, 131, 131, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 495 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082638 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082638 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082638/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082638 Building REAL300000082639 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082639' /scratch/stefan/7930160/working/building/REAL300000082639 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082639 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082639/0 /scratch/stefan/7930160/working/building/REAL300000082639 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/686 `/scratch/stefan/7930160/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=CC=C1F) `REAL300000082639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082639 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 24, 4, 1, 1, 1, 1, 1, 53, 53] 53 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082639 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 44, 44, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 10, 44, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082639 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082639 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082639/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082639 Building REAL300000082640 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082640' /scratch/stefan/7930160/working/building/REAL300000082640 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082640 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082640/0 /scratch/stefan/7930160/working/building/REAL300000082640 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/687 `/scratch/stefan/7930160/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)N1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082640 none COC(=O)C(C)N1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 7, 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, 152, 201, 93, 152, 93, 93, 93, 93, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 152, 152, 152, 152, 93, 93, 93, 30, 9, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082640 none COC(=O)C(C)N1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 7, 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, 13, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 48, 93, 93, 92, 92, 93, 93, 123, 123, 93, 14, 14, 14, 7, 8, 8, 8, 1, 1, 1, 8, 48, 93, 93, 93] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082640 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082640 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082640/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082640 Building REAL300000082641 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082641' /scratch/stefan/7930160/working/building/REAL300000082641 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082641 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082641/0 /scratch/stefan/7930160/working/building/REAL300000082641 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/688 `/scratch/stefan/7930160/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2F)=CC=C1F) `REAL300000082641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082641 none O=C([O-])C1=CC(NN=CC2=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', 'N.pl3', 'N.2', 'C.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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 64, 64, 65, 32, 6, 1, 1, 1, 65, 65] 65 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082641 none O=C([O-])C1=CC(NN=CC2=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', 'N.pl3', 'N.2', 'C.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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 49, 49, 65, 65, 58, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 11, 49, 65, 65, 65, 1, 1] 65 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082641 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082641 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082641/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082641 Building REAL300000082642 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082642' /scratch/stefan/7930160/working/building/REAL300000082642 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082642 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082642/0 /scratch/stefan/7930160/working/building/REAL300000082642 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/689 `/scratch/stefan/7930160/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1) `REAL300000082642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082642 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 71, 148, 201, 201, 201, 201, 201, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 30, 30, 30, 148, 148, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082642 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 30, 44, 44, 30, 1, 1, 1, 5, 17, 40, 40, 40, 40, 40, 2, 2, 2, 2, 2, 2, 1, 30, 30, 30, 1, 1, 1, 17, 17, 40, 40, 40, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 16, 17, 18, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082642 none CC1(C)C(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 40, 14, 4, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 201, 201, 201, 40, 40, 40, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 346 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082642 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082642 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082642/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082642 Building REAL300000082643 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082643' /scratch/stefan/7930160/working/building/REAL300000082643 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082643 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082643/0 /scratch/stefan/7930160/working/building/REAL300000082643 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/690 `/scratch/stefan/7930160/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082643 none CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 174, 67, 174, 67, 67, 67, 67, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 25, 7, 1, 1, 1, 67] 201 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, 43]) total number of confs: 449 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082643 none CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 25, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 31, 67, 67, 67, 67, 67, 67, 94, 94, 66, 1, 29, 29, 29, 28, 28, 28, 29, 29, 29, 1, 1, 1, 7, 31, 67, 67, 67, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 43, 25, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082643 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082643 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082643/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082643 Building REAL300000082644 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082644' /scratch/stefan/7930160/working/building/REAL300000082644 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082644 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082644/0 /scratch/stefan/7930160/working/building/REAL300000082644 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/691 `/scratch/stefan/7930160/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-]) `REAL300000082644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082644 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 157, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 157, 157, 157, 157, 157, 157, 201, 201, 201, 157, 65, 13, 1, 1, 1, 157, 157] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082644 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 63, 157, 157, 156, 156, 157, 157, 201, 201, 157, 1, 1, 1, 1, 2, 2, 4, 4, 4, 1, 12, 63, 157, 157, 157, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 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]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082644 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082644 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082644/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082644 Building REAL300000082645 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082645' /scratch/stefan/7930160/working/building/REAL300000082645 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082645 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082645/0 /scratch/stefan/7930160/working/building/REAL300000082645 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/692 `/scratch/stefan/7930160/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1OC(F)F) `REAL300000082645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082645 none CC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 36, 65, 65, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 65, 65, 110, 201, 201, 65, 65, 65, 65, 65, 65, 35, 8, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082645 none CC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 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, 26, 65, 65, 65, 65, 65, 65, 99, 99, 65, 1, 1, 5, 29, 29, 2, 2, 2, 1, 1, 1, 6, 26, 65, 65, 65, 29] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082645 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082645 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082645/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082645 Building REAL300000082646 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082646' /scratch/stefan/7930160/working/building/REAL300000082646 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082646 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082646/0 /scratch/stefan/7930160/working/building/REAL300000082646 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/693 `/scratch/stefan/7930160/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=CC=C1F) `REAL300000082646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082646 none O=C([O-])C1=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 57, 57, 58, 22, 6, 1, 1, 1, 1, 1, 58, 58] 58 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082646 none O=C([O-])C1=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 11, 41, 58, 58, 58, 58, 58, 1, 1] 58 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082646 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082646 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082646/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082646 Building REAL300000082647 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082647' /scratch/stefan/7930160/working/building/REAL300000082647 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082647 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082647/0 /scratch/stefan/7930160/working/building/REAL300000082647 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/694 `/scratch/stefan/7930160/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1) `REAL300000082647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082647 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 52, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 93, 93, 122, 122, 122, 122, 122, 93, 93, 93, 93, 93, 52, 11, 1, 1, 1, 122, 122, 122, 122, 122] 122 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082647 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 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, 8, 8, 32, 93, 93, 93, 93, 93, 93, 121, 121, 93, 1, 1, 6, 6, 2, 6, 6, 1, 2, 2, 2, 1, 8, 32, 93, 93, 93, 6, 6, 4, 6, 6] 122 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082647 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 18, 18, 55, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 18, 55, 122, 122, 122, 1, 1, 1, 1, 1] 122 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]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082647 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082647 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082647/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082647 Building REAL300000082648 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082648' /scratch/stefan/7930160/working/building/REAL300000082648 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082648 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082648/0 /scratch/stefan/7930160/working/building/REAL300000082648 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/695 `/scratch/stefan/7930160/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082648 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 49, 2, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 39, 39, 39, 39, 39, 39, 67, 67, 39, 7, 7, 49, 48, 49, 49, 49, 49, 49, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 7, 7] 201 rigid atoms, others: [43, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48]) total number of confs: 336 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082648 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 34, 34, 110, 110, 110, 110, 110, 110, 150, 150, 110, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 110, 110, 110, 1, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 47, 48, 35, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 369 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082648 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 65, 65, 110, 110, 39, 39, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 110, 110, 201, 199, 199, 201, 201, 200, 199, 110, 110, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 110, 110] 201 rigid atoms, others: [46, 44, 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, 40, 41, 42, 43, 47, 48]) total number of confs: 645 number of broken/clashed sets: 145 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082648 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082648 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082648/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082648 Building REAL300000082649 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082649' /scratch/stefan/7930160/working/building/REAL300000082649 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082649 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082649/0 /scratch/stefan/7930160/working/building/REAL300000082649 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/696 `/scratch/stefan/7930160/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F) `REAL300000082649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082649 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 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: [49, 34, 49, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 34, 34] 63 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41]) total number of confs: 129 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: REAL300000082649 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 63, 63, 34, 34, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 63, 63, 63, 63, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 336 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082649 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 25, 25, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 63, 63, 63, 63, 63, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 98 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082649 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082649 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082649/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082649 Building REAL300000082650 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082650' /scratch/stefan/7930160/working/building/REAL300000082650 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082650 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082650/0 /scratch/stefan/7930160/working/building/REAL300000082650 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/697 `/scratch/stefan/7930160/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=CC=C23)=CC=C1F) `REAL300000082650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082650 none O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 38 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: REAL300000082650 none O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082650 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082650 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082650/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082650 Building REAL300000082651 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082651' /scratch/stefan/7930160/working/building/REAL300000082651 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082651 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082651/0 /scratch/stefan/7930160/working/building/REAL300000082651 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/698 `/scratch/stefan/7930160/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1) `REAL300000082651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082651 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 7, 30, 63, 63, 63, 1, 1, 6, 6, 6, 6] 65 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 127 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: REAL300000082651 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 11, 11, 40, 65, 65, 65, 65, 65, 65, 65, 65, 65, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 11, 40, 65, 65, 65, 6, 6, 1, 1, 1, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 43, 44, 45, 46, 33, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082651 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 41, 41, 63, 63, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 65, 65, 65, 65, 65, 65, 65, 65, 65, 63, 63, 41, 10, 1, 1, 1, 63, 63, 65, 65, 65, 65] 65 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37, 41, 42, 43, 44, 45, 46]) total number of confs: 206 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082651 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082651/1 /scratch/stefan/7930160/working/building/REAL300000082651 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/699 `/scratch/stefan/7930160/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1) `REAL300000082651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082651 none CN1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 49, 49, 49, 49, 49, 49, 50, 50, 49, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 24, 49, 49, 49, 1, 1, 5, 5, 5, 5] 53 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42, 43, 44, 45]) 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: REAL300000082651 none CN1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 9, 9, 27, 53, 53, 53, 53, 53, 53, 53, 53, 53, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 9, 27, 53, 53, 53, 5, 5, 1, 1, 1, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 42, 43, 44, 45, 24, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082651 none CN1CCN(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 27, 27, 49, 49, 27, 27, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 49, 53, 53, 53, 53, 53, 53, 53, 53, 53, 49, 49, 27, 10, 1, 1, 1, 49, 49, 53, 53, 53, 53] 53 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082651 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082651 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082651/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082651/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082651 Building REAL300000082652 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082652' /scratch/stefan/7930160/working/building/REAL300000082652 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082652 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082652/0 /scratch/stefan/7930160/working/building/REAL300000082652 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/700 `/scratch/stefan/7930160/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1F) `REAL300000082652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082652 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [33, 12, 1, 12, 12, 72, 152, 152, 152, 152, 152, 152, 167, 167, 152, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 72, 152, 152, 152, 1, 1, 1, 1] 180 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 454 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082652 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [101, 38, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 152, 152, 62, 152, 152, 152, 101, 101, 101, 101, 101, 9, 1, 1, 1, 152, 152, 152, 152] 180 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 799 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082652 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082652 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082652/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082652 Building REAL300000082653 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082653' /scratch/stefan/7930160/working/building/REAL300000082653 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082653 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082653/0 /scratch/stefan/7930160/working/building/REAL300000082653 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/701 `/scratch/stefan/7930160/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC) `REAL300000082653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082653 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 9, 1, 9, 9, 49, 149, 149, 149, 149, 149, 149, 175, 175, 149, 1, 1, 1, 1, 1, 1, 1, 1, 3, 27, 27, 27, 27, 27, 49, 149, 149, 149, 1, 2, 2, 2, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 2, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 39, 40, 41]) total number of confs: 449 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082653 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 149, 149, 149, 149, 149, 149, 149, 185, 108, 108, 108, 108, 108, 10, 1, 1, 1, 149, 149, 149, 149, 149, 149, 185, 185, 185] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 572 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082653 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082653 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082653/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082653 Building REAL300000082654 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082654' /scratch/stefan/7930160/working/building/REAL300000082654 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082654 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082654/0 /scratch/stefan/7930160/working/building/REAL300000082654 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/702 `/scratch/stefan/7930160/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1F) `REAL300000082654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082654 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 52, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 52, 120, 120, 120, 1, 1, 1] 120 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000082654 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 120, 120, 120, 120, 120, 120, 120, 47, 47, 47, 10, 1, 1, 1, 120, 120, 120] 120 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082654 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082654 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082654/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082654 Building REAL300000082655 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082655' /scratch/stefan/7930160/working/building/REAL300000082655 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082655 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082655/0 /scratch/stefan/7930160/working/building/REAL300000082655 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/703 `/scratch/stefan/7930160/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1) `REAL300000082655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082655 none CC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 26] 26 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082655 none CC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 1, 1, 1, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42] set([35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082655 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082655 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082655/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082655 Building REAL300000082656 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082656' /scratch/stefan/7930160/working/building/REAL300000082656 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082656 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082656/0 /scratch/stefan/7930160/working/building/REAL300000082656 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/704 `/scratch/stefan/7930160/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1) `REAL300000082656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082656 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 101, 123, 123, 101, 123, 123, 123, 123, 101, 101, 101, 101, 101, 46, 10, 1, 1, 1, 123, 123, 123, 123] 123 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) 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: REAL300000082656 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 40, 101, 101, 101, 101, 101, 101, 122, 122, 101, 1, 1, 6, 6, 1, 3, 6, 6, 6, 1, 2, 2, 2, 1, 9, 40, 101, 101, 101, 6, 6, 6, 6] 123 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082656 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 21, 21, 65, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 21, 65, 123, 123, 123, 1, 1, 1, 1] 123 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 245 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082656 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082656 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082656/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082656 Building REAL300000082657 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082657' /scratch/stefan/7930160/working/building/REAL300000082657 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082657 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082657/0 /scratch/stefan/7930160/working/building/REAL300000082657 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/705 `/scratch/stefan/7930160/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCO1) `REAL300000082657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082657 none CC(C)C1CC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 121, 42, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 42, 42, 1, 1, 1, 125, 125, 125, 125] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082657 none CC(C)C1CC(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 10, 61, 61, 125, 125, 125, 125, 125, 125, 137, 137, 125, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 125, 125, 125, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 39, 40, 41, 19, 20, 21, 38, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082657 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082657 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082657/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082657 Building REAL300000082658 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082658' /scratch/stefan/7930160/working/building/REAL300000082658 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082658 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082658/0 /scratch/stefan/7930160/working/building/REAL300000082658 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/706 `/scratch/stefan/7930160/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082658 none CC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [59, 9, 59, 132, 151, 151, 151, 151, 151, 151, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 59, 59, 59, 132, 132, 151, 151, 151, 151, 1, 1, 1] 151 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082658 none CC(CC1=CC=C(Cl)C=C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 60, 60, 151, 151, 151, 151, 151, 151, 151, 151, 151, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 151, 151, 151] 151 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082658 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082658 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082658/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082658 Building REAL300000082659 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082659' /scratch/stefan/7930160/working/building/REAL300000082659 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082659 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082659/0 /scratch/stefan/7930160/working/building/REAL300000082659 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/707 `/scratch/stefan/7930160/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082659 none CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 163, 116, 163, 53, 53, 53, 53, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1] 201 rigid atoms, others: [43, 44, 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, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082659 none CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 28, 28, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 53, 53, 53, 53, 53, 53, 78, 78, 53, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082659 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082659 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082659/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082659 Building REAL300000082660 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082660' /scratch/stefan/7930160/working/building/REAL300000082660 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082660 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082660/0 /scratch/stefan/7930160/working/building/REAL300000082660 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/708 `/scratch/stefan/7930160/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082660 none CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 68, 69, 69, 68, 68, 36, 68, 68, 68, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 68, 52, 68, 36, 10, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 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]) 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: REAL300000082660 none CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 68, 68, 68, 68, 68, 68, 69, 69, 68, 6, 6, 6, 1, 1, 1, 6, 16, 68, 68, 68] 69 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082660 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082660 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082660/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082660 Building REAL300000082661 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082661' /scratch/stefan/7930160/working/building/REAL300000082661 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082661 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082661/0 /scratch/stefan/7930160/working/building/REAL300000082661 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/709 `/scratch/stefan/7930160/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=[NH+]C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082661 none CN(C)C1=CC=[NH+]C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 6, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 5, 1, 1, 1] 14 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082661 none CN(C)C1=CC=[NH+]C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 6, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 9, 14, 14, 14] 14 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082661 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082661 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082661/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082661 Building REAL300000082662 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082662' /scratch/stefan/7930160/working/building/REAL300000082662 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082662 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082662/0 /scratch/stefan/7930160/working/building/REAL300000082662 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/710 `/scratch/stefan/7930160/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=CC=C1F) `REAL300000082662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082662 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 34, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 4, 5, 5, 5, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24] 47 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38]) total number of confs: 86 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: REAL300000082662 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24, 47, 47, 37, 47, 47, 47, 47, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082662 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 19, 19, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 47, 47] 47 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 71 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082662 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082662 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082662/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082662 Building REAL300000082663 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082663' /scratch/stefan/7930160/working/building/REAL300000082663 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082663 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082663/0 /scratch/stefan/7930160/working/building/REAL300000082663 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/711 `/scratch/stefan/7930160/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082663 none COC(=O)CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 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, 117, 201, 59, 59, 59, 59, 59, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 117, 117, 59, 59, 59, 23, 7, 1, 1, 1] 201 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: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082663 none COC(=O)CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 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: [40, 40, 8, 40, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 59, 59, 58, 58, 59, 59, 84, 84, 59, 40, 40, 40, 8, 8, 1, 1, 1, 8, 33, 59, 59, 59] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082663 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082663 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082663/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082663 Building REAL300000082664 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082664' /scratch/stefan/7930160/working/building/REAL300000082664 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082664 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082664/0 /scratch/stefan/7930160/working/building/REAL300000082664 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/712 `/scratch/stefan/7930160/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=CC=C1F) `REAL300000082664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082664 none O=C([O-])C1=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 199, 109, 39, 39, 7, 1, 1, 1, 1, 1, 39, 64, 64, 51, 64, 64, 199, 199, 199, 199, 199, 109, 7, 7, 1, 1, 1, 1, 1, 1, 1, 64, 64, 51, 64, 64, 199, 199] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 511 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082664 none O=C([O-])C1=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 31, 31, 127, 199, 199, 199, 31, 55, 55, 45, 55, 55, 1, 1, 1, 1, 1, 7, 127, 127, 199, 199, 199, 199, 199, 199, 199, 55, 55, 45, 55, 55, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 760 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082664 none O=C([O-])C1=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 87, 54, 54, 20, 4, 4, 1, 4, 27, 64, 64, 64, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 20, 27, 27, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 54, 54] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 416 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082664 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082664 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082664/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082664 Building REAL300000082665 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082665' /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000082665 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082665/0 /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/713 `/scratch/stefan/7930160/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 3, 14, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 46, 46, 81, 81, 81, 81, 81, 81, 81, 81, 81, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 81, 81, 81] 81 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 137 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: REAL300000082665 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 14, 14, 12, 14, 14, 1, 1, 1, 8, 8, 28, 28, 28, 28, 28, 28, 41, 41, 28, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 1, 28, 28, 28] 81 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 42, 43, 44, 34, 14, 13, 15, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 73, 81, 81, 80, 81, 81, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 28, 28, 28, 28, 28, 28, 73, 73, 81, 81, 81, 81, 81, 28, 28, 28, 1, 1, 1] 81 rigid atoms, others: [45, 46, 47, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 283 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082665/1 /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/714 `/scratch/stefan/7930160/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 3, 14, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 45, 45, 80, 80, 80, 80, 80, 80, 80, 80, 80, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 80, 80, 80] 80 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 136 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: REAL300000082665 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 10, 14, 14, 1, 1, 1, 8, 8, 28, 28, 28, 28, 28, 28, 41, 41, 28, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 14, 14, 10, 14, 14, 1, 1, 1, 28, 28, 28] 80 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 42, 43, 44, 34, 14, 13, 15, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 28, 28, 28, 72, 80, 80, 72, 80, 80, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 28, 28, 28, 28, 28, 28, 72, 72, 80, 80, 72, 80, 80, 28, 28, 28, 1, 1, 1] 80 rigid atoms, others: [45, 46, 47, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 299 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `2' /scratch/stefan/7930160/working/building/REAL300000082665/2 /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 2 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/715 `/scratch/stefan/7930160/working/3D/715' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082665.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 45, 45, 122, 122, 122, 122, 122, 122, 122, 122, 122, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 122, 122, 122] 122 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46]) 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: REAL300000082665 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 55, 55, 33, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 1, 33, 33, 33] 122 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 41, 42, 43, 12, 13, 14, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082665 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 85, 122, 122, 111, 122, 122, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 33, 33, 33, 33, 33, 33, 33, 85, 85, 122, 122, 122, 122, 122, 33, 33, 33, 1, 1, 1] 122 rigid atoms, others: [44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082665 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082665 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082665/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082665/0.* 2: /scratch/stefan/7930160/working/building/REAL300000082665/2.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082665 Building REAL300000082666 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082666' /scratch/stefan/7930160/working/building/REAL300000082666 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082666 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082666/0 /scratch/stefan/7930160/working/building/REAL300000082666 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/716 `/scratch/stefan/7930160/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C(F)=C1) `REAL300000082666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082666 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 171, 171, 171, 171, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 171, 171, 171, 1, 1, 1] 171 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082666 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [56, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 171, 171, 171, 171, 171, 171, 171, 171, 57, 57, 57, 11, 1, 1, 1, 171, 171, 171] 171 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 247 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082666 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082666 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082666/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082666 Building REAL300000082667 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082667' /scratch/stefan/7930160/working/building/REAL300000082667 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082667 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082667/0 /scratch/stefan/7930160/working/building/REAL300000082667 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/717 `/scratch/stefan/7930160/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=CC=C1F) `REAL300000082667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082667 none O=C([O-])C1=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [63, 63, 63, 63, 63, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 34, 8, 2, 1, 1, 1, 1, 1, 63, 63] 126 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 121 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082667 none O=C([O-])C1=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 3, 1, 1, 1, 1, 9, 43, 43, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 9, 43, 126, 63, 63, 63, 63, 63, 1, 1] 126 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: 232 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082667 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082667/1 /scratch/stefan/7930160/working/building/REAL300000082667 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/718 `/scratch/stefan/7930160/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=CC=C1F) `REAL300000082667.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082667 none O=C([O-])C1=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 14, 4, 1, 1, 1, 1, 1, 27, 27] 27 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, 34, 33, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082667 none O=C([O-])C1=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 9, 25, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082667 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082667 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082667/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082667/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082667 Building REAL300000082668 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082668' /scratch/stefan/7930160/working/building/REAL300000082668 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082668 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082668/0 /scratch/stefan/7930160/working/building/REAL300000082668 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/719 `/scratch/stefan/7930160/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1) `REAL300000082668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082668 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 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, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 60, 13, 1, 1, 1, 137, 137, 137, 137] 137 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082668 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 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, 12, 12, 67, 137, 137, 137, 137, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 67, 137, 137, 137, 1, 1, 1, 1] 137 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082668 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082668 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082668/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082668 Building REAL300000082669 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082669' /scratch/stefan/7930160/working/building/REAL300000082669 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082669 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082669/0 /scratch/stefan/7930160/working/building/REAL300000082669 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/720 `/scratch/stefan/7930160/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC=C(Cl)C=C32)=CC=C1F) `REAL300000082669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082669 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 44 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: REAL300000082669 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082669 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082669 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082669/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082669 Building REAL300000082670 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082670' /scratch/stefan/7930160/working/building/REAL300000082670 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082670 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082670/0 /scratch/stefan/7930160/working/building/REAL300000082670 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/721 `/scratch/stefan/7930160/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082670 none NC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 113, 154, 113, 113, 113, 113, 56, 56, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 113, 154, 154, 113, 113, 113, 56, 13, 1, 1, 1, 113] 154 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, 32, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000082670 none NC(=O)C1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 58, 113, 113, 113, 113, 113, 113, 115, 115, 113, 1, 3, 3, 1, 1, 1, 10, 58, 113, 113, 113, 1] 154 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 21, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082670 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082670 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082670/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082670 Building REAL300000082671 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082671' /scratch/stefan/7930160/working/building/REAL300000082671 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082671 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082671/0 /scratch/stefan/7930160/working/building/REAL300000082671 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/722 `/scratch/stefan/7930160/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082671 none CC(=O)NC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 168, 168, 168, 102, 168, 168, 69, 69, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 168, 168, 168, 168, 69, 13, 1, 1, 1] 201 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: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082671 none CC(=O)NC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 66, 168, 168, 168, 168, 168, 168, 177, 177, 168, 4, 4, 4, 4, 1, 1, 1, 1, 11, 66, 168, 168, 168] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082671 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082671 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082671/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082671 Building REAL300000082672 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082672' /scratch/stefan/7930160/working/building/REAL300000082672 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082672 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082672/0 /scratch/stefan/7930160/working/building/REAL300000082672 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/723 `/scratch/stefan/7930160/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=CC=C1F) `REAL300000082672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082672 none O=C([O-])C1=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 71, 69, 69, 33, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 69, 69, 69, 69, 69, 33, 7, 1, 3, 3, 2, 3, 3, 69, 69] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082672 none O=C([O-])C1=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 44, 44, 69, 69, 69, 69, 71, 71, 69, 71, 71, 69, 1, 1, 1, 1, 1, 10, 44, 69, 71, 71, 69, 71, 70, 1, 1] 71 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082672 none O=C([O-])C1=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 42, 17, 17, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 71, 71, 71, 71, 71, 41, 17, 3, 1, 1, 1, 1, 1, 71, 71] 71 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082672 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082672 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082672/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082672 Building REAL300000082673 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082673' /scratch/stefan/7930160/working/building/REAL300000082673 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082673 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082673/0 /scratch/stefan/7930160/working/building/REAL300000082673 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/724 `/scratch/stefan/7930160/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2=NNC=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082673 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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: [11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 61, 61, 61, 61, 61, 61, 91, 91, 61, 11, 11, 11, 11, 11, 11, 11, 1, 1, 8, 33, 61, 61, 61, 11] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 253 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: REAL300000082673 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 38, 38, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 11, 11, 38, 134, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 38, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 438 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082673 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 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, 61, 61, 61, 61, 61, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 61, 61, 27, 7, 1, 1, 1, 201] 201 rigid atoms, others: [35, 36, 37, 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, 38]) total number of confs: 293 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082673 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082673 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082673/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082673 Building REAL300000082674 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082674' /scratch/stefan/7930160/working/building/REAL300000082674 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082674 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082674/0 /scratch/stefan/7930160/working/building/REAL300000082674 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/725 `/scratch/stefan/7930160/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F) `REAL300000082674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082674 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [102, 80, 102, 80, 80, 32, 6, 6, 1, 1, 1, 1, 1, 10, 10, 4, 8, 10, 10, 10, 1, 1, 80, 80, 80, 80, 80, 31, 6, 1, 10, 10, 10, 80, 80] 169 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082674 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 57, 57, 80, 80, 80, 169, 169, 139, 169, 169, 169, 169, 80, 80, 1, 1, 1, 1, 1, 11, 57, 80, 169, 169, 169, 1, 1] 169 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082674 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 169, 94, 29, 29, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 169, 169, 169, 169, 169, 94, 29, 10, 1, 1, 1, 169, 169] 169 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 337 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082674 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082674/1 /scratch/stefan/7930160/working/building/REAL300000082674 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/726 `/scratch/stefan/7930160/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F) `REAL300000082674.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082674 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 138, 99, 99, 50, 50, 8, 1, 1, 1, 1, 1, 8, 8, 1, 4, 8, 8, 8, 1, 1, 99, 99, 99, 99, 99, 8, 8, 1, 8, 8, 8, 99, 99] 201 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300000082674 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 36, 99, 99, 99, 201, 201, 125, 172, 201, 201, 201, 99, 99, 1, 1, 1, 1, 1, 36, 36, 99, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082674 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 136, 136, 33, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 201, 201, 201, 201, 201, 33, 33, 8, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082674 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082674 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082674/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082674/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082674 Building REAL300000082675 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082675' /scratch/stefan/7930160/working/building/REAL300000082675 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082675 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082675/0 /scratch/stefan/7930160/working/building/REAL300000082675 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/727 `/scratch/stefan/7930160/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCO3)S2)=CC=C1F) `REAL300000082675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082675 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [118, 86, 118, 86, 86, 44, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 86, 86, 86, 86, 86, 44, 7, 1, 13, 13, 13, 13, 13, 13, 13, 86, 86] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082675 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 8, 40, 40, 86, 86, 86, 86, 201, 201, 201, 201, 86, 1, 1, 1, 1, 1, 8, 40, 86, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082675 none O=C([O-])C1=CC(NN=CC2=CN=C(C3CCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 151, 54, 54, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 151, 54, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082675 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082675 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082675/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082675 Building REAL300000082676 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082676' /scratch/stefan/7930160/working/building/REAL300000082676 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082676 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082676/0 /scratch/stefan/7930160/working/building/REAL300000082676 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/728 `/scratch/stefan/7930160/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C2(O)CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)C=C1) `REAL300000082676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082676 none CC(C)C1=CC=C(C2(O)CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [13, 2, 13, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 47, 47, 47, 47, 47, 68, 68, 47, 1, 1, 11, 11, 14, 14, 14, 13, 13, 13, 13, 11, 11, 3, 1, 1, 1, 1, 1, 47, 47, 47, 1, 1, 1, 1, 11, 11] 369 rigid atoms, others: [11, 38, 6, 7, 8, 9, 10, 39, 12, 46, 47, 48, 40, 41, 24, 25, 49, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 50, 51]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082676 none CC(C)C1=CC=C(C2(O)CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 49, 49, 112, 112, 112, 112, 112, 112, 117, 117, 112, 11, 11, 1, 1, 3, 3, 3, 2, 2, 2, 2, 1, 1, 33, 11, 11, 11, 11, 11, 112, 112, 112, 11, 11, 11, 11, 1, 1] 369 rigid atoms, others: [1, 3, 4, 5, 6, 7, 50, 35, 36, 26, 27, 51] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082676 none CC(C)C1=CC=C(C2(O)CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [123, 112, 123, 64, 112, 112, 47, 47, 47, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 112, 112, 123, 123, 123, 123, 123, 123, 123, 112, 112, 141, 47, 47, 47, 47, 47, 1, 1, 1, 47, 47, 47, 47, 112, 112] 369 rigid atoms, others: [45, 43, 44, 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, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082676 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082676 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082676/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082676 Building REAL300000082677 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082677' /scratch/stefan/7930160/working/building/REAL300000082677 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082677 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082677/0 /scratch/stefan/7930160/working/building/REAL300000082677 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/729 `/scratch/stefan/7930160/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082677 none CC(C)C1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [78, 50, 78, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 50, 79, 79, 79, 78, 79, 79, 79, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 50] 79 rigid atoms, others: [41, 42, 43, 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, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 254 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: REAL300000082677 none CC(C)C1=CC=C2CCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 76, 76, 50, 1, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 1] 79 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 44] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082677 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082677 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082677/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082677 Building REAL300000082678 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082678' /scratch/stefan/7930160/working/building/REAL300000082678 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082678 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082678/0 /scratch/stefan/7930160/working/building/REAL300000082678 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/730 `/scratch/stefan/7930160/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CC3CCCC4=CC=CC2=C43)=CC=C1F) `REAL300000082678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082678 none O=C([O-])C1=CC(NN=C2CC3CCCC4=CC=CC2=C43)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 32 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 38, 39, 20, 21, 22, 23, 24, 25]) total number of confs: 46 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: REAL300000082678 none O=C([O-])C1=CC(NN=C2CC3CCCC4=CC=CC2=C43)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 55 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082678 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082678 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082678/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082678 Building REAL300000082679 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082679' /scratch/stefan/7930160/working/building/REAL300000082679 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082679 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082679/0 /scratch/stefan/7930160/working/building/REAL300000082679 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/731 `/scratch/stefan/7930160/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082679 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [17, 17, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 49, 49, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 17, 49, 133, 201, 201, 201] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 44, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50]) total number of confs: 423 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: REAL300000082679 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 2, 2, 1, 1, 1, 1, 9, 17, 17, 13, 17, 17, 1, 1, 1, 8, 8, 26, 53, 53, 53, 53, 53, 53, 77, 77, 53, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 17, 1, 8, 26, 53, 53, 53] 201 rigid atoms, others: [1, 4, 5, 6, 7, 45, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 270 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082679 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 157, 201, 201, 180, 201, 201, 53, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 157, 157, 201, 201, 201, 201, 201, 53, 30, 8, 1, 1, 1] 201 rigid atoms, others: [50, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 668 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082679 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082679 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082679/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082679 Building REAL300000082680 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082680' /scratch/stefan/7930160/working/building/REAL300000082680 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082680 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082680/0 /scratch/stefan/7930160/working/building/REAL300000082680 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/732 `/scratch/stefan/7930160/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1) `REAL300000082680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082680 none CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 57, 53, 94, 94, 34, 34, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 94, 94, 94, 201, 200, 198, 94, 94, 34, 34, 34, 9, 1, 1, 1, 94] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 459 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082680 none CSC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 94, 94, 94, 94, 94, 94, 157, 157, 94, 1, 1, 1, 12, 12, 12, 1, 1, 9, 9, 9, 34, 94, 94, 94, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 431 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082680 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082680 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082680/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082680 Building REAL300000082681 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082681' /scratch/stefan/7930160/working/building/REAL300000082681 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082681 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082681/0 /scratch/stefan/7930160/working/building/REAL300000082681 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/733 `/scratch/stefan/7930160/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl) `REAL300000082681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082681 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 100, 100, 100, 1, 1, 1] 100 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000082681 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 100, 100, 52, 72, 100, 100, 100, 52, 52, 52, 11, 1, 1, 1, 100, 100, 100] 100 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082681 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082681 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082681/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082681 Building REAL300000082682 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082682' /scratch/stefan/7930160/working/building/REAL300000082682 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082682 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082682/0 /scratch/stefan/7930160/working/building/REAL300000082682 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/734 `/scratch/stefan/7930160/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=CC=C2C(F)(F)F)=CC=C1F) `REAL300000082682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082682 none O=C([O-])C1=CC(NN=CC2=NC=CC=C2C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 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, 108, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 108, 108, 108, 108, 108, 36, 6, 1, 1, 1, 108, 108] 108 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000082682 none O=C([O-])C1=CC(NN=CC2=NC=CC=C2C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 58, 58, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 11, 58, 108, 108, 108, 1, 1] 108 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082682 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082682 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082682/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082682 Building REAL300000082683 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082683' /scratch/stefan/7930160/working/building/REAL300000082683 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082683 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082683/0 /scratch/stefan/7930160/working/building/REAL300000082683 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/735 `/scratch/stefan/7930160/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2) `REAL300000082683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082683 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 14, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [11, 1, 11, 11, 55, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 107, 107, 107, 1, 1, 1, 1] 107 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 210 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082683 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 14, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [49, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 107, 107, 107, 107, 107, 107, 107, 107, 107, 50, 50, 50, 11, 1, 1, 1, 107, 107, 107, 107] 107 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082683 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082683 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082683/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082683 Building REAL300000082684 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082684' /scratch/stefan/7930160/working/building/REAL300000082684 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082684 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082684/0 /scratch/stefan/7930160/working/building/REAL300000082684 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/736 `/scratch/stefan/7930160/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1) `REAL300000082684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082684 none CCC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 43, 43, 26, 1, 1, 12, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 26, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 39, 40, 41, 22, 23, 42, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 36, 37, 38]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082684 none CCC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 62, 62, 153, 153, 153, 153, 153, 153, 164, 164, 153, 12, 12, 1, 9, 9, 9, 9, 9, 12, 12, 12, 13, 12, 12, 153, 153, 153, 12, 13, 12, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 40, 41, 42]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082684 none CCC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 153, 153, 153, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 26, 153, 201, 201, 201, 201, 201, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082684 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082684 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082684/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082684 Building REAL300000082685 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082685' /scratch/stefan/7930160/working/building/REAL300000082685 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082685 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082685/0 /scratch/stefan/7930160/working/building/REAL300000082685 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/737 `/scratch/stefan/7930160/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1) `REAL300000082685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082685 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [12, 1, 12, 12, 66, 178, 178, 178, 178, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 178, 178, 178, 1, 1, 1] 178 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 315 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: REAL300000082685 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [57, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 178, 178, 178, 178, 178, 178, 178, 58, 58, 58, 11, 1, 1, 1, 178, 178, 178] 178 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 263 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082685 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082685 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082685/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082685 Building REAL300000082686 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082686' /scratch/stefan/7930160/working/building/REAL300000082686 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082686 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082686/0 /scratch/stefan/7930160/working/building/REAL300000082686 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/738 `/scratch/stefan/7930160/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1) `REAL300000082686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082686 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 36, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 36, 89, 89, 89, 1, 2, 2, 1] 89 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 165 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082686 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 89, 89, 89, 48, 48, 89, 89, 89, 48, 48, 48, 10, 1, 1, 1, 89, 89, 89, 89] 89 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 386 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082686 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082686 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082686/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082686 Building REAL300000082687 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082687' /scratch/stefan/7930160/working/building/REAL300000082687 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082687 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082687/0 /scratch/stefan/7930160/working/building/REAL300000082687 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/739 `/scratch/stefan/7930160/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CO2)C=C1) `REAL300000082687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082687 none CC1=CC=C(C2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 3, 3, 1, 1, 1, 1, 1, 7, 7, 33, 76, 76, 76, 76, 76, 76, 80, 80, 76, 1, 1, 3, 3, 4, 4, 4, 3, 3, 7, 33, 76, 76, 76, 1, 3, 3] 80 rigid atoms, others: [35, 4, 5, 6, 7, 8, 21, 22] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082687 none CC1=CC=C(C2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 4, 4, 4, 19, 19, 53, 80, 80, 80, 80, 80, 80, 80, 80, 80, 4, 4, 1, 1, 2, 2, 2, 1, 1, 19, 52, 80, 80, 80, 4, 1, 1] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 36, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082687 none CC1=CC=C(C2=NC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [77, 76, 80, 80, 76, 76, 76, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 76, 76, 80, 80, 80, 80, 80, 80, 79, 50, 10, 1, 1, 1, 76, 80, 80] 80 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082687 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082687 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082687/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082687 Building REAL300000082688 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082688' /scratch/stefan/7930160/working/building/REAL300000082688 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082688 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082688/0 /scratch/stefan/7930160/working/building/REAL300000082688 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/740 `/scratch/stefan/7930160/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082688 none CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 59, 59, 73, 73, 73, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 73, 73, 73, 73, 73, 73, 73, 73, 43, 13, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082688 none CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 74, 74, 74, 74, 74, 74, 74, 74, 74, 2, 2, 2, 1, 1, 2, 2, 2, 7, 39, 74, 74, 74] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082688 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082688 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082688/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082688 Building REAL300000082689 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082689' /scratch/stefan/7930160/working/building/REAL300000082689 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082689 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082689/0 /scratch/stefan/7930160/working/building/REAL300000082689 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/741 `/scratch/stefan/7930160/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1C1=CC=CC=C1) `REAL300000082689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082689 none CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 57, 75, 75, 74, 75, 75, 57, 57, 57, 57, 32, 8, 1, 1, 1, 75, 75, 75, 75, 75] 75 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082689 none CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 28, 57, 57, 57, 57, 57, 57, 75, 75, 57, 1, 1, 4, 4, 2, 4, 4, 2, 2, 2, 1, 9, 27, 57, 57, 57, 4, 4, 3, 4, 4] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082689 none CC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [4, 4, 4, 4, 4, 4, 12, 12, 36, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 36, 75, 75, 75, 1, 1, 1, 1, 1] 75 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082689 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082689 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082689/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082689 Building REAL300000082690 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082690' /scratch/stefan/7930160/working/building/REAL300000082690 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082690 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082690/0 /scratch/stefan/7930160/working/building/REAL300000082690 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/742 `/scratch/stefan/7930160/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C) `REAL300000082690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082690 none CCCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 81, 81, 81, 81, 81, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 81, 81, 201, 201, 201, 201, 201, 189, 189, 81, 81, 81, 27, 7, 1, 1, 1, 81, 81, 81] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082690 none CCCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 81, 81, 81, 81, 81, 81, 124, 124, 81, 1, 1, 10, 10, 10, 9, 9, 5, 5, 2, 2, 2, 11, 45, 81, 81, 81, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 22] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082690 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082690 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082690/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082690 Building REAL300000082691 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082691' /scratch/stefan/7930160/working/building/REAL300000082691 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082691 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082691/0 /scratch/stefan/7930160/working/building/REAL300000082691 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/743 `/scratch/stefan/7930160/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082691 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 36, 74, 74, 74, 74, 75, 75, 75, 75, 75, 4, 4, 4, 1, 1, 1, 1, 3, 8, 37, 74, 74, 75] 75 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082691 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 1, 6, 6, 34, 74, 74, 74, 74, 74, 74, 75, 75, 74, 2, 2, 2, 3, 3, 3, 3, 1, 6, 34, 74, 74, 74] 75 rigid atoms, others: [0, 1, 2, 3, 4, 33, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082691 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 74, 74, 74, 74, 74, 38, 10, 1, 1, 1] 75 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082691 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082691 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082691/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082691 Building REAL300000082692 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082692' /scratch/stefan/7930160/working/building/REAL300000082692 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082692 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082692/0 /scratch/stefan/7930160/working/building/REAL300000082692 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/744 `/scratch/stefan/7930160/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=CC=C1F) `REAL300000082692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082692 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 70, 105, 70, 70, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 70, 70, 70, 70, 70, 37, 10, 1, 1, 11, 11, 11, 11, 70, 70] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 294 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: REAL300000082692 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 26, 26, 70, 70, 70, 70, 70, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7, 26, 70, 70, 201, 201, 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: 290 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082692 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 140, 44, 44, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 140, 44, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 450 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082692 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082692 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082692/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082692 Building REAL300000082693 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082693' /scratch/stefan/7930160/working/building/REAL300000082693 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082693 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082693/0 /scratch/stefan/7930160/working/building/REAL300000082693 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/745 `/scratch/stefan/7930160/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21) `REAL300000082693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082693 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [92, 92, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 53, 13, 1, 1, 1, 92, 92, 92] 92 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082693 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 9, 9, 44, 92, 92, 91, 91, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 44, 92, 92, 92, 1, 1, 1] 92 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082693 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082693/1 /scratch/stefan/7930160/working/building/REAL300000082693 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/746 `/scratch/stefan/7930160/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082693.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082693 none CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 142, 142, 142, 141, 141, 141, 49, 49, 1, 1, 1] 142 rigid atoms, others: [32, 33, 34, 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]) 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: REAL300000082693 none CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 62, 62, 141, 141, 141, 141, 141, 141, 142, 142, 141, 2, 2, 2, 1, 1, 1, 8, 8, 141, 141, 141] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082693 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082693 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082693/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082693/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082693 Building REAL300000082694 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082694' /scratch/stefan/7930160/working/building/REAL300000082694 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082694 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082694/0 /scratch/stefan/7930160/working/building/REAL300000082694 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/747 `/scratch/stefan/7930160/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=CC=C1F) `REAL300000082694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082694 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 104, 75, 75, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 75, 75, 75, 75, 75, 39, 9, 1, 1, 11, 11, 11, 11, 75, 75] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082694 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 30, 30, 75, 75, 75, 75, 75, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 30, 75, 75, 201, 201, 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: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082694 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 143, 37, 37, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 37, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 448 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082694 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082694 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082694/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082694 Building REAL300000082695 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082695' /scratch/stefan/7930160/working/building/REAL300000082695 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082695 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082695/0 /scratch/stefan/7930160/working/building/REAL300000082695 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/748 `/scratch/stefan/7930160/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=CC=C1F) `REAL300000082695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082695 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [145, 105, 145, 105, 105, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 105, 105, 105, 105, 105, 45, 8, 1, 1, 6, 6, 6, 105, 105] 171 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082695 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 11, 45, 45, 105, 105, 105, 105, 105, 171, 171, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 11, 45, 105, 105, 171, 171, 171, 1, 1] 171 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082695 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 118, 26, 26, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 118, 26, 7, 7, 1, 1, 1, 178, 178] 178 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 385 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082695 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082695 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082695/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082695 Building REAL300000082696 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082696' /scratch/stefan/7930160/working/building/REAL300000082696 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082696 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082696/0 /scratch/stefan/7930160/working/building/REAL300000082696 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/749 `/scratch/stefan/7930160/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F) `REAL300000082696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082696 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [109, 75, 109, 75, 75, 29, 7, 7, 1, 1, 1, 1, 1, 12, 12, 9, 12, 12, 12, 12, 1, 1, 75, 75, 75, 75, 75, 29, 7, 1, 12, 12, 11, 75, 75] 175 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300000082696 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 53, 53, 75, 75, 75, 175, 175, 165, 175, 175, 175, 175, 75, 75, 1, 1, 1, 1, 1, 11, 53, 74, 175, 175, 175, 1, 1] 175 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082696 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 175, 100, 32, 32, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 175, 175, 175, 175, 175, 100, 32, 12, 1, 1, 1, 175, 175] 175 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 350 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082696 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082696/1 /scratch/stefan/7930160/working/building/REAL300000082696 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/750 `/scratch/stefan/7930160/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F) `REAL300000082696.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082696 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 129, 101, 101, 48, 48, 8, 1, 1, 1, 1, 1, 7, 7, 5, 7, 7, 7, 7, 1, 1, 101, 101, 101, 101, 101, 8, 8, 1, 7, 7, 7, 101, 101] 201 rigid atoms, others: [8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082696 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 40, 101, 101, 101, 201, 201, 189, 201, 201, 201, 201, 101, 101, 1, 1, 1, 1, 1, 40, 40, 101, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082696 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 131, 131, 32, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 32, 32, 7, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 351 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082696 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082696 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082696/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082696/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082696 Building REAL300000082697 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082697' /scratch/stefan/7930160/working/building/REAL300000082697 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082697 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082697/0 /scratch/stefan/7930160/working/building/REAL300000082697 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/751 `/scratch/stefan/7930160/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=CC=C1F) `REAL300000082697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082697 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [156, 117, 156, 117, 117, 47, 9, 9, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 47, 9, 8, 8, 8, 8, 8, 1, 1, 117, 117] 188 rigid atoms, others: [32, 33, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082697 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 64, 64, 117, 117, 188, 188, 117, 117, 117, 117, 117, 82, 1, 1, 1, 1, 1, 12, 64, 188, 188, 188, 188, 188, 117, 117, 1, 1] 188 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082697 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 114, 34, 34, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 188, 188, 188, 188, 188, 114, 34, 1, 1, 1, 1, 1, 8, 8, 188, 188] 188 rigid atoms, others: [10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082697 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082697 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082697/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082697 Building REAL300000082698 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082698' /scratch/stefan/7930160/working/building/REAL300000082698 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082698 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082698/0 /scratch/stefan/7930160/working/building/REAL300000082698 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/752 `/scratch/stefan/7930160/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=CC=C1F) `REAL300000082698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082698 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [85, 55, 85, 55, 55, 13, 13, 1, 1, 1, 1, 1, 13, 13, 5, 13, 13, 13, 1, 55, 55, 55, 55, 55, 1, 1, 1, 1, 13, 13, 12, 13, 1, 1, 55, 55] 172 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 28, 29, 30, 31, 34, 35]) total number of confs: 231 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: REAL300000082698 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 55, 55, 55, 172, 172, 165, 172, 172, 172, 55, 1, 1, 1, 1, 1, 55, 55, 55, 55, 172, 172, 172, 172, 55, 55, 1, 1] 172 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082698 none O=C([O-])C1=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 85, 85, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 172, 172, 172, 172, 172, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 172, 172] 172 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 248 number of broken/clashed sets: 30 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082698 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082698 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082698/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082698 Building REAL300000082699 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082699' /scratch/stefan/7930160/working/building/REAL300000082699 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082699 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082699/0 /scratch/stefan/7930160/working/building/REAL300000082699 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/753 `/scratch/stefan/7930160/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)C)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2) `REAL300000082699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082699 none CC1=CC=C(C(C)C)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 76, 76, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 53, 53, 54, 54, 54, 53, 53, 76, 77, 77, 77, 77, 77, 77, 10, 1, 1, 1, 53, 53, 53, 53] 77 rigid atoms, others: [39, 40, 41, 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, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 236 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: REAL300000082699 none CC1=CC=C(C(C)C)C2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 77, 77, 53, 1, 1, 1, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 9, 53, 53, 53, 1, 1, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 45, 44, 43, 42, 23, 24, 25, 29, 30] set([6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082699 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082699 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082699/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082699 Building REAL300000082700 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082700' /scratch/stefan/7930160/working/building/REAL300000082700 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082700 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082700/0 /scratch/stefan/7930160/working/building/REAL300000082700 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/754 `/scratch/stefan/7930160/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=CC=C1F) `REAL300000082700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082700 none O=C([O-])C1=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 173, 110, 110, 51, 13, 3, 1, 1, 1, 1, 1, 1, 1, 110, 147, 147, 110, 138, 147, 147, 201, 201, 201, 201, 201, 173, 51, 51, 3, 3, 1, 1, 1, 1, 1, 147, 147, 147, 147, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 837 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082700 none O=C([O-])C1=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 15, 55, 91, 172, 201, 201, 184, 201, 201, 15, 24, 24, 15, 21, 24, 24, 1, 1, 1, 1, 1, 4, 55, 55, 172, 172, 201, 201, 201, 201, 201, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082700 none O=C([O-])C1=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 32, 24, 24, 11, 4, 4, 1, 4, 22, 45, 102, 147, 147, 113, 147, 147, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 11, 22, 22, 102, 102, 147, 147, 147, 147, 147, 1, 1, 1, 1, 24, 24] 201 rigid atoms, others: [8, 41, 42, 43, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 655 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082700 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082700 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082700/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082700 Building REAL300000082701 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082701' /scratch/stefan/7930160/working/building/REAL300000082701 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082701 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082701/0 /scratch/stefan/7930160/working/building/REAL300000082701 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/755 `/scratch/stefan/7930160/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(CC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082701 none CCC1=NN(C)C(CC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 86, 86, 86, 86, 86, 86, 86, 131, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 136, 136, 136, 136, 136, 86, 86, 86, 131, 131, 131, 131, 131, 23, 6, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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, 35, 36, 37]) total number of confs: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082701 none CCC1=NN(C)C(CC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 11, 11, 59, 86, 86, 86, 86, 86, 86, 113, 113, 86, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 3, 3, 3, 11, 59, 86, 86, 86] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082701 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082701 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082701/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082701 Building REAL300000082702 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082702' /scratch/stefan/7930160/working/building/REAL300000082702 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082702 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082702/0 /scratch/stefan/7930160/working/building/REAL300000082702 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/756 `/scratch/stefan/7930160/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=CC=C1F) `REAL300000082702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082702 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 42, 41, 41, 16, 4, 4, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 41, 41, 41, 41, 41, 16, 4, 3, 3, 1, 3, 3, 1, 1, 41, 41] 42 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082702 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 36, 36, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 10, 36, 41, 41, 41, 41, 41, 41, 41, 1, 1] 42 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082702 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 42, 41, 41, 18, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 41, 41, 41, 18, 8, 1, 1, 1, 1, 1, 3, 3, 41, 41] 42 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082702 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082702 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082702/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082702 Building REAL300000082703 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082703' /scratch/stefan/7930160/working/building/REAL300000082703 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082703 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082703/0 /scratch/stefan/7930160/working/building/REAL300000082703 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/757 `/scratch/stefan/7930160/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082703 none CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 9, 34, 62, 129, 188, 188, 151, 188, 188, 188, 188, 188, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 34, 62, 62, 188, 188, 151, 188, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 640 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: REAL300000082703 none CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 49, 131, 131, 188, 188, 188, 188, 188, 188, 201, 201, 188, 60, 60, 60, 60, 60, 49, 28, 28, 1, 1, 1, 1, 188, 188, 188] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 532 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082703 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082703 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082703/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082703 Building REAL300000082704 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082704' /scratch/stefan/7930160/working/building/REAL300000082704 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082704 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082704/0 /scratch/stefan/7930160/working/building/REAL300000082704 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/758 `/scratch/stefan/7930160/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082704 none CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 7, 7, 7, 4, 7, 7, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 193, 193, 193, 196, 196, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 193, 193, 193, 193, 196, 196, 196, 196, 196, 196, 196, 61, 12, 1, 1, 1] 196 rigid atoms, others: [37, 38, 39, 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]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082704 none CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 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, 7, 7, 7, 4, 7, 7, 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 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, 1, 2, 2, 1, 1, 13, 13, 82, 193, 193, 193, 193, 193, 193, 196, 196, 193, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 13, 82, 193, 193, 193] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 24] set([8, 9, 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: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082704 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082704 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082704/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082704 Building REAL300000082705 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082705' /scratch/stefan/7930160/working/building/REAL300000082705 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082705 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082705/0 /scratch/stefan/7930160/working/building/REAL300000082705 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/759 `/scratch/stefan/7930160/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000082705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082705 none CS(=O)(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 79, 122, 122, 21, 4, 1, 4, 4, 14, 27, 27, 27, 27, 27, 27, 47, 47, 27, 1, 1, 1, 1, 1, 1, 122, 122, 122, 79, 21, 21, 14, 27, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 19, 20, 21, 22, 23, 24, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 559 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082705 none CS(=O)(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 201, 201, 69, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 14, 27, 27, 20, 27, 27, 201, 201, 201, 165, 69, 69, 4, 1, 1, 1, 27, 27, 19, 27, 27] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082705 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082705 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082705/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082705 Building REAL300000082706 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082706' /scratch/stefan/7930160/working/building/REAL300000082706 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082706 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082706/0 /scratch/stefan/7930160/working/building/REAL300000082706 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/760 `/scratch/stefan/7930160/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082706 none CN1C=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 88, 88, 88, 89, 89, 89, 88, 88, 52, 10, 1, 1, 1, 88, 88] 89 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: 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: REAL300000082706 none CN1C=NC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 88, 88, 88, 88, 88, 88, 89, 89, 88, 1, 1, 1, 2, 2, 2, 1, 1, 8, 42, 88, 88, 88, 1, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 20, 21, 22, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082706 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082706 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082706/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082706 Building REAL300000082707 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082707' /scratch/stefan/7930160/working/building/REAL300000082707 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082707 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082707/0 /scratch/stefan/7930160/working/building/REAL300000082707 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/761 `/scratch/stefan/7930160/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1) `REAL300000082707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082707 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 13, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082707 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 201, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 40, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082707 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082707 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082707/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082707 Building REAL300000082708 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082708' /scratch/stefan/7930160/working/building/REAL300000082708 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082708 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082708/0 /scratch/stefan/7930160/working/building/REAL300000082708 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/762 `/scratch/stefan/7930160/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC=C1[N+](=O)[O-])C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082708 none CC(CC1=CC=CC=C1[N+](=O)[O-])C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 41, 96, 163, 201, 201, 201, 201, 201, 201, 201, 201, 9, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 100, 100, 100, 100, 163, 163, 201, 201, 201, 201, 41, 41, 41, 41, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 821 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082708 none CC(CC1=CC=CC=C1[N+](=O)[O-])C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 21, 21, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 21, 21, 21, 21, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 357 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082708 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082708 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082708/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082708 Building REAL300000082709 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082709' /scratch/stefan/7930160/working/building/REAL300000082709 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082709 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082709/0 /scratch/stefan/7930160/working/building/REAL300000082709 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/763 `/scratch/stefan/7930160/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1) `REAL300000082709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082709 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 184, 166, 39, 166, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 39, 201, 201, 201, 201, 201, 39, 39, 39, 39, 39, 39, 1, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082709 none CCOC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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: [62, 33, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 39, 39, 39, 39, 39, 39, 58, 58, 39, 1, 1, 1, 63, 63, 63, 62, 62, 1, 1, 1, 1, 1, 1, 39, 39, 39, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 42, 43, 21, 22, 23, 38, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 35, 36, 37, 39, 40, 41]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082709 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082709 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082709/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082709 Building REAL300000082710 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082710' /scratch/stefan/7930160/working/building/REAL300000082710 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082710 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082710/0 /scratch/stefan/7930160/working/building/REAL300000082710 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/764 `/scratch/stefan/7930160/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Br) `REAL300000082710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082710 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 121, 121, 121, 121, 121, 121, 121, 121, 53, 13, 1, 1, 1, 121] 121 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082710 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 58, 121, 121, 120, 120, 121, 121, 121, 121, 121, 1, 1, 1, 2, 2, 2, 1, 1, 10, 58, 121, 121, 121, 1] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082710 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082710 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082710/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082710 Building REAL300000082711 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082711' /scratch/stefan/7930160/working/building/REAL300000082711 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082711 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082711/0 /scratch/stefan/7930160/working/building/REAL300000082711 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/765 `/scratch/stefan/7930160/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCOC3=CC(Br)=CC=C32)=CC=C1F) `REAL300000082711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082711 none O=C([O-])C1=CC(NN=C2CCOC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) 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: REAL300000082711 none O=C([O-])C1=CC(NN=C2CCOC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082711 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082711 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082711/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082711 Building REAL300000082712 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082712' /scratch/stefan/7930160/working/building/REAL300000082712 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082712 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082712/0 /scratch/stefan/7930160/working/building/REAL300000082712 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/766 `/scratch/stefan/7930160/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC2(CC1)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1O2) `REAL300000082712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082712 none C[NH+]1CCC2(CC1)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 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, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [45, 11, 44, 43, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49]) total number of confs: 21 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: REAL300000082712 none C[NH+]1CCC2(CC1)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1O2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 1, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49] set([45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 19 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082712 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082712 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082712/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082712 Building REAL300000082713 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082713' /scratch/stefan/7930160/working/building/REAL300000082713 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082713 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082713/0 /scratch/stefan/7930160/working/building/REAL300000082713 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/767 `/scratch/stefan/7930160/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000082713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082713 none CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 46, 25, 101, 101, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 101, 101, 101, 101, 201, 201, 201, 199, 200, 101, 101, 25, 25, 25, 7, 1, 1, 1, 101] 201 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40]) total number of confs: 718 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082713 none CCOC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 51, 101, 101, 101, 101, 101, 101, 143, 143, 101, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 1, 1, 13, 13, 13, 51, 101, 101, 101, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 427 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082713 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082713 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082713/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082713 Building REAL300000082714 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082714' /scratch/stefan/7930160/working/building/REAL300000082714 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082714 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082714/0 /scratch/stefan/7930160/working/building/REAL300000082714 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/768 `/scratch/stefan/7930160/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=CC=C2Br)=CC=C1F) `REAL300000082714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082714 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 50, 10, 1, 1, 1, 76, 76] 76 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082714 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 40, 40, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 10, 40, 76, 76, 76, 1, 1] 76 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082714 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082714 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082714/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082714 Building REAL300000082715 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082715' /scratch/stefan/7930160/working/building/REAL300000082715 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082715 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082715/0 /scratch/stefan/7930160/working/building/REAL300000082715 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/769 `/scratch/stefan/7930160/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=CC=C1F) `REAL300000082715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082715 none O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 32, 32] 32 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 44 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: REAL300000082715 none O=C([O-])C1=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 10, 32, 32, 32, 32, 32, 32, 1, 1] 32 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082715 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082715 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082715/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082715 Building REAL300000082716 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082716' /scratch/stefan/7930160/working/building/REAL300000082716 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082716 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082716/0 /scratch/stefan/7930160/working/building/REAL300000082716 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/770 `/scratch/stefan/7930160/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=CC=C1F) `REAL300000082716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082716 none O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 30, 30] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 42 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: REAL300000082716 none O=C([O-])C1=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 1, 1] 30 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 53 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082716 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082716 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082716/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082716 Building REAL300000082717 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082717' /scratch/stefan/7930160/working/building/REAL300000082717 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082717 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082717/0 /scratch/stefan/7930160/working/building/REAL300000082717 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/771 `/scratch/stefan/7930160/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-]) `REAL300000082717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082717 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 17, 39, 39, 39, 1, 1, 1] 39 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000082717 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39, 29, 29, 29, 6, 1, 1, 1, 39, 39, 39] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082717 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082717 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082717/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082717 Building REAL300000082718 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082718' /scratch/stefan/7930160/working/building/REAL300000082718 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082718 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082718/0 /scratch/stefan/7930160/working/building/REAL300000082718 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/772 `/scratch/stefan/7930160/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082718 none CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 51, 13, 1, 1, 1] 128 rigid atoms, others: [41, 42, 43, 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, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082718 none CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 12, 64, 128, 128, 128, 128, 128, 128, 128, 128, 128, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 64, 128, 128, 128] 128 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082718 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082718 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082718/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082718 Building REAL300000082719 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082719' /scratch/stefan/7930160/working/building/REAL300000082719 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082719 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082719/0 /scratch/stefan/7930160/working/building/REAL300000082719 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/773 `/scratch/stefan/7930160/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2)=CC=C1F) `REAL300000082719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082719 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 57, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114, 114, 113, 113, 114, 57, 8, 1, 1, 1, 114, 114] 114 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082719 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 50, 50, 114, 114, 85, 114, 114, 114, 114, 1, 1, 1, 1, 1, 13, 50, 114, 114, 114, 1, 1] 114 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: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082719 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082719 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082719/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082719 Building REAL300000082720 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082720' /scratch/stefan/7930160/working/building/REAL300000082720 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082720 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082720/0 /scratch/stefan/7930160/working/building/REAL300000082720 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/774 `/scratch/stefan/7930160/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C(F)(F)F)=C2)=CC=C1F) `REAL300000082720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082720 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 56, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 132, 132, 131, 131, 132, 56, 10, 1, 1, 1, 132, 132] 132 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000082720 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 56, 56, 132, 132, 98, 132, 132, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 13, 56, 132, 132, 132, 1, 1] 132 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: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082720 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082720 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082720/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082720 Building REAL300000082721 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082721' /scratch/stefan/7930160/working/building/REAL300000082721 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082721 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082721/0 /scratch/stefan/7930160/working/building/REAL300000082721 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/775 `/scratch/stefan/7930160/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=C1) `REAL300000082721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082721 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 138, 61, 61, 62, 62, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 159, 159, 159, 159, 159, 62, 62, 44, 10, 1, 1, 1, 62] 159 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) 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: REAL300000082721 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 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, 6, 1, 1, 1, 1, 1, 1, 8, 8, 24, 62, 62, 62, 62, 62, 62, 92, 92, 62, 1, 1, 13, 13, 13, 12, 12, 1, 1, 8, 24, 62, 62, 62, 1] 159 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 20, 21, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082721 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082721 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082721/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082721 Building REAL300000082722 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082722' /scratch/stefan/7930160/working/building/REAL300000082722 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082722 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082722/0 /scratch/stefan/7930160/working/building/REAL300000082722 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/776 `/scratch/stefan/7930160/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)S1) `REAL300000082722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082722 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 111, 111, 111, 111, 111, 111, 112, 112, 111, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 54, 111, 111, 111, 1, 1] 112 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082722 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 111, 111, 111, 111, 111, 111, 51, 51, 51, 10, 1, 1, 1, 111, 111] 112 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082722 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082722 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082722/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082722 Building REAL300000082723 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082723' /scratch/stefan/7930160/working/building/REAL300000082723 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082723 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082723/0 /scratch/stefan/7930160/working/building/REAL300000082723 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/777 `/scratch/stefan/7930160/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082723 none CC(C)C1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 47, 69, 47, 47, 47, 47, 47, 47, 47, 47, 46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 69, 69, 69, 69, 69, 69, 47, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1] 69 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: 210 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: REAL300000082723 none CC(C)C1=CC=CC2=C1OCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 46, 46, 47, 47, 69, 69, 47, 3, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47] 69 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 12, 13, 14, 11, 35, 36, 38, 37] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42]) total number of confs: 174 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082723 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082723 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082723/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082723 Building REAL300000082724 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082724' /scratch/stefan/7930160/working/building/REAL300000082724 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082724 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082724/0 /scratch/stefan/7930160/working/building/REAL300000082724 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/778 `/scratch/stefan/7930160/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=CC=C1F) `REAL300000082724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082724 none O=C([O-])C1=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 30, 52, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 30, 30] 52 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 134 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: REAL300000082724 none O=C([O-])C1=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 30, 52, 52, 30, 52, 52, 30, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 52, 52, 30, 52, 52, 30, 30, 1, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082724 none O=C([O-])C1=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 18, 18, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 52, 52, 52, 52, 52, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 52, 52] 52 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]) total number of confs: 74 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082724 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082724 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082724/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082724 Building REAL300000082725 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082725' /scratch/stefan/7930160/working/building/REAL300000082725 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082725 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082725/0 /scratch/stefan/7930160/working/building/REAL300000082725 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/779 `/scratch/stefan/7930160/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC3(CC2)NC(=O)NC3=O)=CC=C1F) `REAL300000082725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082725 none O=C([O-])C1=CC(N=NC2CCC3(CC2)NC(=O)NC3=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 36, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082725 none O=C([O-])C1=CC(N=NC2CCC3(CC2)NC(=O)NC3=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 24 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082725 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082725 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082725/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082725 Building REAL300000082726 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082726' /scratch/stefan/7930160/working/building/REAL300000082726 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082726 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082726/0 /scratch/stefan/7930160/working/building/REAL300000082726 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/780 `/scratch/stefan/7930160/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082726 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 29, 63, 63, 63, 63, 63, 63, 63, 63, 63, 4, 4, 4, 1, 1, 1, 1, 1, 4, 9, 29, 63, 63, 63] 63 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082726 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 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, 4, 4, 2, 4, 4, 1, 1, 1, 6, 6, 24, 62, 62, 62, 62, 62, 62, 63, 63, 62, 2, 2, 2, 4, 4, 2, 4, 4, 1, 6, 24, 62, 62, 62] 63 rigid atoms, others: [0, 1, 2, 3, 4, 33, 10, 11, 12] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082726 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 63, 63, 63, 63, 63, 62, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 63, 63, 63, 63, 62, 40, 9, 1, 1, 1] 63 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082726 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082726 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082726/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082726 Building REAL300000082727 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082727' /scratch/stefan/7930160/working/building/REAL300000082727 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082727 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082727/0 /scratch/stefan/7930160/working/building/REAL300000082727 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/781 `/scratch/stefan/7930160/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082727 none COC1=CC=CC(OC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 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: [163, 131, 131, 131, 49, 131, 131, 131, 178, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 163, 163, 163, 131, 50, 131, 178, 178, 178, 48, 10, 1, 1, 1] 201 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 487 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082727 none COC1=CC=CC(OC)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 4, 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 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, 3, 1, 1, 11, 11, 32, 71, 71, 71, 71, 71, 71, 93, 93, 71, 3, 3, 3, 1, 1, 1, 4, 4, 4, 11, 32, 71, 71, 71] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 26, 27, 28] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082727 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082727 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082727/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082727 Building REAL300000082728 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082728' /scratch/stefan/7930160/working/building/REAL300000082728 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082728 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082728/0 /scratch/stefan/7930160/working/building/REAL300000082728 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/782 `/scratch/stefan/7930160/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082728 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 45, 11, 1, 1, 1, 94, 94, 94, 94] 94 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082728 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 53, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 52, 94, 94, 94, 1, 1, 1, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 34, 17, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082728 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082728 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082728/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082728 Building REAL300000082729 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082729' /scratch/stefan/7930160/working/building/REAL300000082729 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082729 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082729/0 /scratch/stefan/7930160/working/building/REAL300000082729 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/783 `/scratch/stefan/7930160/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=CC=C21) `REAL300000082729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082729 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 51, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 51, 13, 1, 1, 1, 84, 84, 84, 84] 84 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082729 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 47, 84, 84, 83, 83, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 47, 84, 84, 84, 1, 1, 1, 1] 84 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082729 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082729/1 /scratch/stefan/7930160/working/building/REAL300000082729 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/784 `/scratch/stefan/7930160/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082729.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082729 none CN1C2=CC=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [148, 148, 148, 148, 148, 148, 148, 148, 148, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 149, 149, 149, 148, 148, 148, 148, 47, 47, 1, 1, 1] 149 rigid atoms, others: [32, 33, 34, 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]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082729 none CN1C2=CC=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 64, 65, 149, 149, 149, 149, 149, 149, 149, 149, 149, 2, 2, 2, 1, 1, 1, 1, 8, 8, 149, 149, 149] 149 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082729 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082729 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082729/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082729/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082729 Building REAL300000082730 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082730' /scratch/stefan/7930160/working/building/REAL300000082730 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082730 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082730/0 /scratch/stefan/7930160/working/building/REAL300000082730 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/785 `/scratch/stefan/7930160/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082730 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 43, 67, 67, 67, 67, 67, 67, 67, 67, 67, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 67, 67, 67] 67 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44]) total number of confs: 149 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: REAL300000082730 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 32, 62, 62, 62, 62, 62, 62, 64, 64, 62, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 31, 62, 62, 62] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13] set([7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082730 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 67, 67, 67, 67, 67, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 62, 62, 62, 62, 67, 67, 67, 67, 67, 67, 67, 67, 32, 9, 1, 1, 1] 67 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082730 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082730 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082730/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082730 Building REAL300000082731 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082731' /scratch/stefan/7930160/working/building/REAL300000082731 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082731 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082731/0 /scratch/stefan/7930160/working/building/REAL300000082731 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/786 `/scratch/stefan/7930160/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2Cl)=CC=C1F) `REAL300000082731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082731 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 260 conformations in input total number of sets (complete confs): 260 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 71, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 71, 12, 2, 1, 1, 1, 130, 130] 260 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 255 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: REAL300000082731 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 260 conformations in input total number of sets (complete confs): 260 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 49, 50, 130, 130, 130, 104, 130, 130, 130, 1, 1, 1, 1, 1, 10, 49, 260, 130, 130, 130, 1, 1] 260 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 564 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082731 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082731 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082731/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082731 Building REAL300000082732 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082732' /scratch/stefan/7930160/working/building/REAL300000082732 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082732 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082732/0 /scratch/stefan/7930160/working/building/REAL300000082732 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/787 `/scratch/stefan/7930160/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(N3CCOCC3)S2)=CC=C1F) `REAL300000082732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082732 none O=C([O-])C1=CC(NN=CC2=CN=C(N3CCOCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [80, 63, 80, 63, 63, 34, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 63, 63, 63, 63, 63, 34, 7, 1, 12, 12, 12, 13, 12, 13, 12, 12, 63, 63] 135 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082732 none O=C([O-])C1=CC(NN=CC2=CN=C(N3CCOCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 32, 32, 63, 63, 63, 63, 135, 135, 135, 134, 135, 63, 1, 1, 1, 1, 1, 6, 32, 63, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1] 135 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082732 none O=C([O-])C1=CC(NN=CC2=CN=C(N3CCOCC3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 135, 107, 45, 45, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 135, 135, 135, 135, 135, 106, 45, 12, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135] 135 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082732 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082732 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082732/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082732 Building REAL300000082733 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082733' /scratch/stefan/7930160/working/building/REAL300000082733 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082733 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082733/0 /scratch/stefan/7930160/working/building/REAL300000082733 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/788 `/scratch/stefan/7930160/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=NC2=NN1) `REAL300000082733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082733 none CC1=C2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 4, 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, 55, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 55, 13, 1, 1, 1, 119, 119] 119 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082733 none CC1=C2C=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=NC2=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 57, 119, 119, 118, 118, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 57, 119, 119, 119, 1, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 18, 19, 20, 21, 22, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082733 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082733 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082733/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082733 Building REAL300000082734 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082734' /scratch/stefan/7930160/working/building/REAL300000082734 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082734 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082734/0 /scratch/stefan/7930160/working/building/REAL300000082734 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/789 `/scratch/stefan/7930160/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082734 none CN(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 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 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 48, 54, 48, 48, 48, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 54, 54, 54, 54, 54, 54, 48, 25, 9, 1, 1, 1] 54 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082734 none CN(C)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 23, 48, 48, 47, 47, 48, 48, 57, 57, 48, 1, 4, 4, 4, 4, 4, 4, 1, 6, 23, 48, 48, 48] 57 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082734 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082734 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082734/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082734 Building REAL300000082735 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082735' /scratch/stefan/7930160/working/building/REAL300000082735 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082735 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082735/0 /scratch/stefan/7930160/working/building/REAL300000082735 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/790 `/scratch/stefan/7930160/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F) `REAL300000082735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 4, 4, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 49, 49, 49, 49, 49, 14, 4, 1, 4, 4, 1, 4, 4, 49, 49] 49 rigid atoms, others: [8, 9, 10, 11, 12, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 42, 42, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 13, 42, 49, 49, 49, 49, 49, 49, 1, 1] 49 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 17, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 17, 7, 4, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082735 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082735/1 /scratch/stefan/7930160/working/building/REAL300000082735 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/791 `/scratch/stefan/7930160/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F) `REAL300000082735.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 191, 191, 69, 69, 9, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 191, 191, 191, 191, 191, 9, 9, 1, 4, 4, 2, 4, 4, 191, 191] 201 rigid atoms, others: [8, 9, 10, 11, 12, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 65, 191, 191, 191, 201, 201, 191, 201, 201, 191, 191, 1, 1, 1, 1, 1, 65, 65, 191, 201, 201, 191, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082735 none O=C([O-])C1=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 114, 114, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201, 201, 201, 19, 19, 4, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 313 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082735 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082735 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082735/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082735/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082735 Building REAL300000082736 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082736' /scratch/stefan/7930160/working/building/REAL300000082736 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082736 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082736/0 /scratch/stefan/7930160/working/building/REAL300000082736 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/792 `/scratch/stefan/7930160/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F) `REAL300000082736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082736 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 115, 164, 115, 115, 59, 59, 8, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 115, 115, 115, 115, 115, 8, 8, 6, 6, 1, 6, 6, 1, 115, 115] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082736 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 29, 114, 114, 115, 201, 201, 115, 201, 201, 114, 114, 1, 1, 1, 1, 1, 29, 29, 201, 201, 123, 201, 201, 114, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082736 none O=C([O-])C1=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 141, 141, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 34, 34, 1, 1, 1, 1, 1, 6, 201, 201] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34]) total number of confs: 357 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082736 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082736/1 /scratch/stefan/7930160/working/building/REAL300000082736 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/793 `/scratch/stefan/7930160/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F) `REAL300000082736.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082736 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [74, 60, 74, 60, 60, 20, 7, 7, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 60, 60, 60, 60, 60, 20, 7, 6, 6, 1, 6, 6, 1, 60, 60] 101 rigid atoms, others: [32, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) 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: REAL300000082736 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 38, 38, 60, 60, 60, 101, 101, 95, 101, 101, 60, 60, 1, 1, 1, 1, 1, 10, 38, 101, 101, 95, 101, 101, 60, 1, 1] 101 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082736 none O=C([O-])C1=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 59, 25, 25, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 101, 101, 101, 101, 101, 58, 25, 1, 1, 1, 1, 1, 6, 101, 101] 101 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34]) total number of confs: 215 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082736 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082736 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082736/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082736/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082736 Building REAL300000082737 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082737' /scratch/stefan/7930160/working/building/REAL300000082737 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082737 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082737/0 /scratch/stefan/7930160/working/building/REAL300000082737 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/794 `/scratch/stefan/7930160/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C) `REAL300000082737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082737 none CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 108, 108, 108, 108, 108, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 187, 187, 187, 187, 187, 108, 108, 108, 33, 11, 1, 1, 1, 108, 108, 108] 187 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082737 none CCN1N=C(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 108, 108, 108, 108, 108, 108, 138, 138, 108, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 10, 48, 108, 108, 108, 2, 2, 2] 187 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082737 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082737 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082737/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082737 Building REAL300000082738 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082738' /scratch/stefan/7930160/working/building/REAL300000082738 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082738 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082738/0 /scratch/stefan/7930160/working/building/REAL300000082738 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/795 `/scratch/stefan/7930160/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C2OC(C)CC2=C1) `REAL300000082738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082738 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [96, 70, 70, 70, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 70, 70, 70, 70, 70, 70, 70, 97, 97, 97, 70, 52, 10, 1, 1, 1, 70, 71, 71, 71, 70, 70, 70] 97 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000082738 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 8, 8, 33, 70, 70, 70, 70, 70, 70, 97, 97, 70, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 8, 33, 70, 70, 70, 1, 2, 2, 2, 1, 1, 1] 97 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 34, 18, 19, 20, 21, 22, 23, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082738 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082738 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082738/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082738 Building REAL300000082739 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082739' /scratch/stefan/7930160/working/building/REAL300000082739 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082739 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082739/0 /scratch/stefan/7930160/working/building/REAL300000082739 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/796 `/scratch/stefan/7930160/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=CC=C1F) `REAL300000082739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082739 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 53 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: REAL300000082739 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082739 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082739 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082739/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082739 Building REAL300000082740 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082740' /scratch/stefan/7930160/working/building/REAL300000082740 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082740 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082740/0 /scratch/stefan/7930160/working/building/REAL300000082740 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/797 `/scratch/stefan/7930160/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21) `REAL300000082740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082740 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 55, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 55, 13, 1, 1, 1, 104, 104, 104] 104 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082740 none CN1C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 11, 11, 53, 104, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 53, 104, 104, 104, 1, 1, 1] 104 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082740 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082740/1 /scratch/stefan/7930160/working/building/REAL300000082740 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/798 `/scratch/stefan/7930160/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082740.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082740 none CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 161, 161, 161, 160, 160, 160, 49, 49, 1, 1, 1] 161 rigid atoms, others: [32, 33, 34, 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]) 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: REAL300000082740 none CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 64, 64, 160, 160, 160, 160, 160, 160, 161, 161, 160, 2, 2, 2, 1, 1, 1, 8, 8, 160, 160, 160] 161 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082740 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082740 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082740/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082740/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082740 Building REAL300000082741 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082741' /scratch/stefan/7930160/working/building/REAL300000082741 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082741 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082741/0 /scratch/stefan/7930160/working/building/REAL300000082741 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/799 `/scratch/stefan/7930160/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)OC(C)(C)C)C1COCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082741 none CC(NC(=O)OC(C)(C)C)C1COCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 55, 118, 158, 158, 201, 201, 201, 201, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 55, 55, 55, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1] 201 rigid atoms, others: [51, 50, 17, 18, 19, 20, 21, 22, 23, 24, 52, 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, 45, 46, 47, 48, 49]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082741 none CC(NC(=O)OC(C)(C)C)C1COCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 14, 25, 25, 37, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 49, 49, 31, 5, 5, 5, 4, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31] 201 rigid atoms, others: [1, 45, 43, 16, 44, 10, 11, 12, 13, 14, 15, 48, 49, 46, 47, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 50, 51, 52]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082741 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082741 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082741/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082741 Building REAL300000082742 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082742' /scratch/stefan/7930160/working/building/REAL300000082742 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082742 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082742/0 /scratch/stefan/7930160/working/building/REAL300000082742 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/800 `/scratch/stefan/7930160/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1) `REAL300000082742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082742 none COCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 7, 1, 7, 30, 30, 88, 88, 88, 88, 88, 88, 129, 129, 88, 1, 1, 1, 1, 1, 1, 60, 60, 60, 25, 25, 16, 16, 7, 88, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082742 none COCCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 75, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 88, 88, 88, 88, 85, 165, 165, 165, 116, 120, 79, 79, 37, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 799 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082742 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082742 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082742/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082742 Building REAL300000082743 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082743' /scratch/stefan/7930160/working/building/REAL300000082743 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082743 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082743/0 /scratch/stefan/7930160/working/building/REAL300000082743 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/801 `/scratch/stefan/7930160/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082743 none CC1=CC(Cl)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 72, 88, 88, 88, 55, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 88, 88, 88, 88, 88, 88, 55, 13, 1, 1, 1] 88 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: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082743 none CC1=CC(Cl)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 10, 10, 46, 88, 88, 88, 88, 88, 88, 88, 88, 88, 2, 2, 2, 1, 1, 1, 10, 46, 88, 88, 88] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082743 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082743 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082743/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082743 Building REAL300000082744 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082744' /scratch/stefan/7930160/working/building/REAL300000082744 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082744 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082744/0 /scratch/stefan/7930160/working/building/REAL300000082744 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/802 `/scratch/stefan/7930160/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C) `REAL300000082744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082744 none CC(C)OC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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, 107, 116, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 50, 50, 116, 116, 116, 116, 116, 116, 116, 50, 50, 50, 50, 1, 1, 1, 50, 50, 50, 50, 50, 50] 116 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082744 none CC(C)OC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 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: [15, 6, 15, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 78, 78, 50, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 50, 50, 50, 2, 2, 2, 2, 2, 2] 116 rigid atoms, others: [32, 3, 4, 5, 6, 7, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082744 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082744 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082744/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082744 Building REAL300000082745 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082745' /scratch/stefan/7930160/working/building/REAL300000082745 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082745 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082745/0 /scratch/stefan/7930160/working/building/REAL300000082745 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/803 `/scratch/stefan/7930160/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1) `REAL300000082745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082745 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 89, 89, 89, 89, 89, 89, 106, 106, 89, 1, 1, 1, 1, 1, 3, 7, 7, 7, 1, 1, 6, 6, 6, 30, 89, 89, 89, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 134 rigid atoms, others: [32, 1, 33, 43, 44, 14, 15, 16, 17, 18, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 240 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082745 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 89, 89, 31, 31, 132, 134, 134, 134, 89, 89, 32, 32, 32, 8, 1, 1, 1, 89, 89, 134, 134, 134, 134, 134, 134, 134, 134, 134, 89, 89] 134 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082745 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082745 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082745/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082745 Building REAL300000082746 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082746' /scratch/stefan/7930160/working/building/REAL300000082746 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082746 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082746/0 /scratch/stefan/7930160/working/building/REAL300000082746 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/804 `/scratch/stefan/7930160/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=CC=C1F) `REAL300000082746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082746 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 33, 10, 1, 1, 1, 1, 1, 1, 63, 63] 63 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082746 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 42, 42, 63, 63, 63, 62, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 10, 42, 63, 62, 63, 63, 63, 63, 1, 1] 63 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082746 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082746 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082746/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082746 Building REAL300000082747 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082747' /scratch/stefan/7930160/working/building/REAL300000082747 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082747 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082747/0 /scratch/stefan/7930160/working/building/REAL300000082747 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/805 `/scratch/stefan/7930160/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=CC(Br)=C2)=CC=C1F) `REAL300000082747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082747 none O=C([O-])C1=CC(NN=CC2=CN=CC(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 107, 58, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 107, 58, 8, 1, 1, 1, 108, 108] 108 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 26, 27]) 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: REAL300000082747 none O=C([O-])C1=CC(NN=CC2=CN=CC(Br)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 46, 46, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 10, 46, 107, 107, 107, 1, 1] 108 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082747 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082747 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082747/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082747 Building REAL300000082748 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082748' /scratch/stefan/7930160/working/building/REAL300000082748 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082748 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082748/0 /scratch/stefan/7930160/working/building/REAL300000082748 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/806 `/scratch/stefan/7930160/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082748 none CCCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 162, 96, 36, 36, 36, 36, 36, 36, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 198, 198, 162, 162, 36, 36, 36, 36, 19, 5, 1, 1, 1] 201 rigid atoms, others: [39, 40, 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, 38]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082748 none CCCCOC1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [76, 50, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 36, 36, 36, 36, 36, 36, 48, 48, 36, 77, 77, 77, 74, 73, 65, 65, 31, 31, 1, 1, 1, 1, 4, 18, 36, 36, 36] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082748 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082748 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082748/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082748 Building REAL300000082749 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082749' /scratch/stefan/7930160/working/building/REAL300000082749 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082749 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082749/0 /scratch/stefan/7930160/working/building/REAL300000082749 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/807 `/scratch/stefan/7930160/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(C(F)(F)F)CC2)=CC=C1F) `REAL300000082749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082749 none O=C([O-])C1=CC(N=NC2CCC(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 20, 21, 22]) 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: REAL300000082749 none O=C([O-])C1=CC(N=NC2CCC(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082749 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082749 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082749/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082749 Building REAL300000082750 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082750' /scratch/stefan/7930160/working/building/REAL300000082750 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082750 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082750/0 /scratch/stefan/7930160/working/building/REAL300000082750 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/808 `/scratch/stefan/7930160/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1) `REAL300000082750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 47, 47, 100, 119, 119, 109, 119, 119, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 47, 47, 100, 100, 119, 119, 119, 119, 119, 47, 47] 119 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 425 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: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 47, 47, 47, 47, 47, 47, 68, 68, 47, 1, 1, 1, 1, 9, 13, 13, 11, 13, 13, 1, 2, 2, 2, 1, 1, 1, 1, 47, 47, 47, 1, 1, 9, 9, 13, 13, 13, 13, 13, 1, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 46, 47, 16, 17, 18, 19, 26, 37, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 195 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 13, 13, 72, 72, 119, 119, 119, 119, 119, 119, 119, 119, 119, 12, 3, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 119, 119, 119, 13, 13, 3, 3, 1, 1, 1, 1, 1, 13, 13] 119 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 192 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082750 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082750/1 /scratch/stefan/7930160/working/building/REAL300000082750 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/809 `/scratch/stefan/7930160/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1) `REAL300000082750.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 20, 20, 20, 51, 63, 63, 56, 63, 63, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 51, 51, 63, 63, 63, 63, 63, 20, 20] 63 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 241 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: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 20, 20, 20, 20, 20, 20, 32, 32, 20, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 2, 2, 2, 1, 1, 1, 1, 20, 20, 20, 1, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 46, 47, 16, 17, 18, 19, 26, 37, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082750 none CC1CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 14, 42, 42, 63, 63, 63, 63, 63, 63, 63, 63, 63, 14, 3, 14, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 63, 63, 63, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14] 63 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 112 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082750 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082750 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082750/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082750/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082750 Building REAL300000082751 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082751' /scratch/stefan/7930160/working/building/REAL300000082751 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082751 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082751/0 /scratch/stefan/7930160/working/building/REAL300000082751 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/810 `/scratch/stefan/7930160/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082751 none CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 29, 48, 68, 68, 68, 68, 68, 68, 160, 160, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 29, 29, 48, 48, 68, 68, 68, 68, 68, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [51, 50, 17, 18, 19, 20, 21, 22, 23, 24, 52, 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, 45, 46, 47, 48, 49]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082751 none CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 16, 16, 16, 7, 36, 36, 68, 68, 68, 68, 68, 68, 97, 97, 68, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 68, 68, 68] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 39, 34, 40, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082751 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082751 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082751/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082751 Building REAL300000082752 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082752' /scratch/stefan/7930160/working/building/REAL300000082752 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082752 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082752/0 /scratch/stefan/7930160/working/building/REAL300000082752 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/811 `/scratch/stefan/7930160/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2CCC(C(F)(F)F)CC2)=CC=C1F) `REAL300000082752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082752 none O=C([O-])C1=CC(N=NCC2CCC(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 53, 53, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 123, 123, 123, 123, 123, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123] 123 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 37, 36]) total number of confs: 190 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082752 none O=C([O-])C1=CC(N=NCC2CCC(C(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 56, 123, 123, 114, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 56, 56, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 436 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082752 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082752 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082752/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082752 Building REAL300000082753 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082753' /scratch/stefan/7930160/working/building/REAL300000082753 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082753 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082753/0 /scratch/stefan/7930160/working/building/REAL300000082753 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/812 `/scratch/stefan/7930160/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Br)C=CS2)=CC=C1F) `REAL300000082753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082753 none O=C([O-])C1=CC(NN=CC2=C(Br)C=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.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, 8, 8, 1, 1, 1, 17, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 82, 44, 11, 1, 1, 83, 83] 83 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 24, 25]) 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: REAL300000082753 none O=C([O-])C1=CC(NN=CC2=C(Br)C=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.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, 8, 8, 1, 1, 1, 17, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 48, 48, 82, 83, 82, 82, 82, 1, 1, 1, 1, 1, 12, 48, 83, 82, 1, 1] 83 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082753 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082753 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082753/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082753 Building REAL300000082754 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082754' /scratch/stefan/7930160/working/building/REAL300000082754 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082754 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082754/0 /scratch/stefan/7930160/working/building/REAL300000082754 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/813 `/scratch/stefan/7930160/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F) `REAL300000082754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082754 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 63, 148, 148, 148, 148, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 148, 148, 148, 1, 1] 148 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 278 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082754 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 148, 148, 148, 60, 148, 148, 148, 51, 51, 51, 10, 1, 1, 1, 148, 148] 148 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 368 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082754 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082754 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082754/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082754 Building REAL300000082755 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082755' /scratch/stefan/7930160/working/building/REAL300000082755 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082755 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082755/0 /scratch/stefan/7930160/working/building/REAL300000082755 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/814 `/scratch/stefan/7930160/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1O) `REAL300000082755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082755 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 242 conformations in input total number of sets (complete confs): 242 using faster count positions algorithm for large data unique positions, atoms: [121, 89, 89, 89, 89, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 89, 89, 89, 89, 121, 121, 121, 89, 89, 48, 10, 1, 1, 1, 178] 242 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082755 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Br)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 242 conformations in input total number of sets (complete confs): 242 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 38, 89, 89, 89, 89, 89, 89, 121, 121, 89, 1, 1, 1, 1, 4, 4, 4, 1, 1, 8, 38, 89, 89, 89, 2] 242 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082755 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082755 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082755/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082755 Building REAL300000082756 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082756' /scratch/stefan/7930160/working/building/REAL300000082756 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082756 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082756/0 /scratch/stefan/7930160/working/building/REAL300000082756 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/815 `/scratch/stefan/7930160/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082756 none COC(=O)C1=COC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 4, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 63, 105, 63, 63, 63, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 105, 105, 105, 63, 27, 9, 1, 1, 1, 63] 105 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082756 none COC(=O)C1=COC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 4, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 37, 63, 63, 62, 62, 63, 63, 66, 66, 63, 1, 11, 11, 11, 1, 6, 37, 63, 63, 63, 1] 105 rigid atoms, others: [2, 4, 5, 6, 7, 8, 21, 25, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082756 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082756 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082756/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082756 Building REAL300000082757 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082757' /scratch/stefan/7930160/working/building/REAL300000082757 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082757 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082757/0 /scratch/stefan/7930160/working/building/REAL300000082757 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/816 `/scratch/stefan/7930160/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-]) `REAL300000082757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082757 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 19, 63, 63, 63, 1, 1, 1] 63 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000082757 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 63, 63, 63, 59, 63, 63, 63, 63, 63, 47, 47, 47, 10, 1, 1, 1, 63, 60, 63] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082757 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082757 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082757/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082757 Building REAL300000082758 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082758' /scratch/stefan/7930160/working/building/REAL300000082758 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082758 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082758/0 /scratch/stefan/7930160/working/building/REAL300000082758 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/817 `/scratch/stefan/7930160/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=CC=C1F) `REAL300000082758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082758 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 56, 78, 56, 56, 27, 6, 6, 1, 1, 1, 1, 1, 1, 13, 36, 36, 36, 36, 1, 1, 1, 56, 56, 56, 56, 56, 27, 6, 1, 1, 36, 36, 1, 56, 56] 201 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082758 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 19, 19, 56, 56, 56, 56, 131, 201, 201, 201, 201, 56, 56, 56, 1, 1, 1, 1, 1, 5, 19, 56, 56, 201, 201, 56, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082758 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082758 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082758/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082758 Building REAL300000082759 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082759' /scratch/stefan/7930160/working/building/REAL300000082759 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082759 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082759/0 /scratch/stefan/7930160/working/building/REAL300000082759 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/818 `/scratch/stefan/7930160/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F) `REAL300000082759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082759 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [32, 13, 1, 13, 13, 70, 161, 161, 161, 161, 161, 161, 178, 178, 161, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 70, 161, 161, 161, 1, 1, 1] 197 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 461 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082759 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [104, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 161, 161, 161, 161, 161, 161, 161, 105, 105, 105, 104, 104, 8, 1, 1, 1, 161, 161, 161] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 523 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082759 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082759 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082759/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082759 Building REAL300000082760 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082760' /scratch/stefan/7930160/working/building/REAL300000082760 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082760 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082760/0 /scratch/stefan/7930160/working/building/REAL300000082760 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/819 `/scratch/stefan/7930160/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=CC=C1F) `REAL300000082760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082760 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [47, 33, 47, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 33, 33] 52 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38]) total number of confs: 105 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: REAL300000082760 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 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: [3, 1, 3, 1, 1, 1, 1, 8, 8, 33, 33, 33, 33, 33, 52, 52, 33, 52, 52, 52, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 52, 52, 33, 52, 1, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082760 none O=C([O-])C1=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 19, 19, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 52, 52] 52 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 73 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082760 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082760 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082760/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082760 Building REAL300000082761 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082761' /scratch/stefan/7930160/working/building/REAL300000082761 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082761 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082761/0 /scratch/stefan/7930160/working/building/REAL300000082761 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/820 `/scratch/stefan/7930160/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)C=CC=C23)=CC=C1F) `REAL300000082761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082761 none O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 55 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: REAL300000082761 none O=C([O-])C1=CC(NN=C2CCCC3=C(Cl)C=CC=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082761 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082761 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082761/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082761 Building REAL300000082762 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082762' /scratch/stefan/7930160/working/building/REAL300000082762 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082762 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082762/0 /scratch/stefan/7930160/working/building/REAL300000082762 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/821 `/scratch/stefan/7930160/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1)OCO2) `REAL300000082762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082762 none COC1=CC2=C(C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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, 118, 118, 118, 118, 118, 118, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 118, 118, 131, 133, 133, 118, 118, 65, 13, 1, 1, 1, 118, 118] 133 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) 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: REAL300000082762 none COC1=CC2=C(C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 49, 118, 118, 117, 117, 118, 118, 133, 133, 118, 1, 1, 1, 4, 4, 4, 1, 1, 11, 49, 118, 118, 118, 1, 1] 133 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082762 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082762 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082762/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082762 Building REAL300000082763 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082763' /scratch/stefan/7930160/working/building/REAL300000082763 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082763 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082763/0 /scratch/stefan/7930160/working/building/REAL300000082763 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/822 `/scratch/stefan/7930160/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2F)=CC=C1F) `REAL300000082763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082763 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 117, 117, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 39, 39, 8, 8, 1, 1, 1, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000082763 none O=C([O-])C1=CC(N=NC=CCC2=CC=C(F)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 30, 30, 99, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 29, 30, 99, 99, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082763 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082763 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082763/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082763 Building REAL300000082764 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082764' /scratch/stefan/7930160/working/building/REAL300000082764 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082764 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082764/0 /scratch/stefan/7930160/working/building/REAL300000082764 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/823 `/scratch/stefan/7930160/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCOC3=CC(F)=CC=C32)=CC=C1F) `REAL300000082764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082764 none O=C([O-])C1=CC(NN=C2CCCOC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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, 32, 33, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082764 none O=C([O-])C1=CC(NN=C2CCCOC3=CC(F)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082764 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082764 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082764/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082764 Building REAL300000082765 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082765' /scratch/stefan/7930160/working/building/REAL300000082765 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082765 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082765/0 /scratch/stefan/7930160/working/building/REAL300000082765 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/824 `/scratch/stefan/7930160/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082765 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 32, 80, 80, 80, 80, 80, 80, 97, 97, 80, 7, 7, 7, 3, 1, 1, 1, 1, 1, 3, 3, 7, 32, 80, 80, 80] 97 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000082765 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 4, 4, 20, 57, 57, 57, 57, 57, 57, 76, 76, 57, 4, 4, 4, 1, 3, 3, 1, 3, 3, 1, 1, 4, 20, 57, 57, 57] 97 rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 13, 14, 36, 30, 37] set([0, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082765 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [79, 57, 57, 57, 38, 57, 80, 80, 57, 80, 80, 57, 57, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 79, 57, 80, 80, 80, 80, 80, 57, 57, 38, 11, 1, 1, 1] 97 rigid atoms, others: [40, 41, 42, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 380 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082765 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082765 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082765/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082765 Building REAL300000082766 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082766' /scratch/stefan/7930160/working/building/REAL300000082766 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082766 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082766/0 /scratch/stefan/7930160/working/building/REAL300000082766 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/825 `/scratch/stefan/7930160/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=CC=C1F) `REAL300000082766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082766 none O=C([O-])C1=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 44, 67, 44, 44, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 44, 44, 44, 44, 44, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 44, 44] 67 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 28, 29, 30, 31, 34, 35]) total number of confs: 152 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082766 none O=C([O-])C1=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 44, 44, 44, 67, 67, 67, 67, 67, 67, 44, 1, 1, 1, 1, 1, 44, 44, 44, 44, 67, 67, 67, 67, 44, 44, 1, 1] 67 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082766 none O=C([O-])C1=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 29, 29, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 67, 67, 67, 67, 67, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 67, 67] 67 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082766 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082766 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082766/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082766 Building REAL300000082767 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082767' /scratch/stefan/7930160/working/building/REAL300000082767 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082767 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082767/0 /scratch/stefan/7930160/working/building/REAL300000082767 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/826 `/scratch/stefan/7930160/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-]) `REAL300000082767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082767 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [62, 34, 34, 34, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 34, 34, 127, 174, 176, 193, 185, 62, 62, 62, 34, 14, 4, 1, 1, 1, 34, 34, 174, 174, 176, 176] 201 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 551 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082767 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 19, 34, 34, 34, 34, 34, 34, 48, 48, 34, 1, 1, 1, 1, 9, 35, 37, 56, 53, 3, 3, 3, 1, 7, 19, 34, 34, 34, 1, 1, 35, 35, 37, 37] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 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, 38, 39, 40, 41]) total number of confs: 325 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082767 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082767 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082767/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082767 Building REAL300000082768 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082768' /scratch/stefan/7930160/working/building/REAL300000082768 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082768 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082768/0 /scratch/stefan/7930160/working/building/REAL300000082768 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/827 `/scratch/stefan/7930160/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082768 none CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 158, 113, 158, 53, 53, 53, 53, 53, 53, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 187, 187, 187, 187, 187, 187, 187, 187, 187, 113, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1] 187 rigid atoms, others: [51, 49, 50, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082768 none CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 23, 27, 27, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 53, 53, 84, 84, 53, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53] 187 rigid atoms, others: [45, 11, 15, 37, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 48, 40, 46, 43, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50, 51]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082768 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082768 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082768/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082768 Building REAL300000082769 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082769' /scratch/stefan/7930160/working/building/REAL300000082769 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082769 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082769/0 /scratch/stefan/7930160/working/building/REAL300000082769 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/828 `/scratch/stefan/7930160/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082769 none CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 39, 81, 119, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 39, 39, 88, 88, 112, 119, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 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]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082769 none CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 31, 8, 8, 5, 5, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082769 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082769 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082769/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082769 Building REAL300000082770 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082770' /scratch/stefan/7930160/working/building/REAL300000082770 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082770 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082770/0 /scratch/stefan/7930160/working/building/REAL300000082770 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/829 `/scratch/stefan/7930160/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(SC(F)F)C=C2)=CC=C1F) `REAL300000082770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082770 none O=C([O-])C1=CC(NN=CC2=CC=C(SC(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 59, 40, 40, 17, 3, 3, 1, 1, 1, 1, 1, 1, 12, 47, 47, 1, 1, 40, 40, 40, 40, 40, 16, 3, 1, 1, 47, 1, 1, 40, 40] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082770 none O=C([O-])C1=CC(NN=CC2=CC=C(SC(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 29, 29, 40, 40, 29, 40, 164, 201, 201, 40, 40, 1, 1, 1, 1, 1, 7, 29, 40, 40, 201, 40, 40, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082770 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082770 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082770/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082770 Building REAL300000082771 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082771' /scratch/stefan/7930160/working/building/REAL300000082771 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082771 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082771/0 /scratch/stefan/7930160/working/building/REAL300000082771 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/830 `/scratch/stefan/7930160/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=CC=C1F) `REAL300000082771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082771 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 71, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 147, 147, 148, 71, 12, 1, 1, 1, 1, 1, 148, 148] 148 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000082771 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 49, 49, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 11, 49, 148, 148, 148, 148, 148, 1, 1] 148 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 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/7930160/working/building/REAL300000082771 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082771 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082771/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082771 Building REAL300000082772 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082772' /scratch/stefan/7930160/working/building/REAL300000082772 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082772 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082772/0 /scratch/stefan/7930160/working/building/REAL300000082772 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/831 `/scratch/stefan/7930160/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC[NH+](CCC(F)(F)F)CC2)=CC=C1F) `REAL300000082772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082772 none O=C([O-])C1=CC(N=NC2CC[NH+](CCC(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 31, 53, 31, 31, 13, 13, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 4, 4, 6, 6, 1, 1, 1, 1, 31, 31] 103 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 19, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 31, 32, 33, 34, 39, 40]) total number of confs: 156 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082772 none O=C([O-])C1=CC(N=NC2CC[NH+](CCC(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 61, 103, 103, 103, 103, 31, 31, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 61, 61, 103, 103, 31, 31, 31, 31, 1, 1] 103 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 484 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082772 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082772/1 /scratch/stefan/7930160/working/building/REAL300000082772 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/832 `/scratch/stefan/7930160/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCN(CCC(F)(F)F)CC2)=CC=C1F) `REAL300000082772.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082772 none O=C([O-])C1=CC(N=NC2CCN(CCC(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [49, 35, 49, 35, 35, 13, 13, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 6, 6, 8, 8, 1, 1, 1, 1, 35, 35] 101 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 30, 31, 32, 33, 38, 39]) total number of confs: 134 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082772 none O=C([O-])C1=CC(N=NC2CCN(CCC(F)(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 10, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 35, 35, 35, 35, 77, 101, 101, 101, 101, 35, 35, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 77, 77, 101, 101, 35, 35, 35, 35, 1, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 433 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082772 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082772 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082772/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082772/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082772 Building REAL300000082773 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082773' /scratch/stefan/7930160/working/building/REAL300000082773 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082773 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082773/0 /scratch/stefan/7930160/working/building/REAL300000082773 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/833 `/scratch/stefan/7930160/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1) `REAL300000082773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 15, 15, 27, 27, 27, 27, 27, 27, 37, 37, 27, 1, 1, 1, 1, 1, 1, 5, 9, 9, 5, 9, 9, 1, 4, 4, 4, 4, 27, 27, 27, 1, 1, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 1, 1] 57 rigid atoms, others: [1, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 46, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 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: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 27, 27, 27, 27, 27, 50, 57, 57, 50, 57, 57, 27, 22, 22, 22, 22, 1, 1, 1, 27, 27, 27, 27, 27, 50, 50, 57, 57, 50, 57, 57, 27, 27] 57 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 234 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 9, 15, 39, 39, 57, 57, 57, 57, 57, 57, 57, 57, 57, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 57, 57, 57, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9] 57 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 127 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082773 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082773/1 /scratch/stefan/7930160/working/building/REAL300000082773 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/834 `/scratch/stefan/7930160/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1) `REAL300000082773.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 15, 15, 27, 27, 27, 27, 27, 27, 38, 38, 27, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 1, 4, 4, 4, 4, 27, 27, 27, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 1] 58 rigid atoms, others: [1, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 46, 26, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 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: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 27, 27, 27, 27, 27, 51, 58, 58, 58, 58, 58, 27, 22, 22, 22, 22, 1, 1, 1, 27, 27, 27, 27, 27, 51, 51, 58, 58, 58, 58, 58, 27, 27] 58 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082773 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 16, 40, 40, 58, 58, 58, 58, 58, 58, 58, 58, 58, 9, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 58, 58, 58, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 9, 9] 58 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 134 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082773 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082773 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082773/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082773/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082773 Building REAL300000082774 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082774' /scratch/stefan/7930160/working/building/REAL300000082774 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082774 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082774/0 /scratch/stefan/7930160/working/building/REAL300000082774 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/835 `/scratch/stefan/7930160/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082774 none CC(C)(C)OC(=O)NC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 201, 126, 75, 126, 23, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 23, 23, 23, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 23, 23, 23, 9, 1, 1, 1, 23, 23, 23, 23] 201 rigid atoms, others: [45, 44, 43, 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, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49]) total number of confs: 527 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082774 none CC(C)(C)OC(=O)NC1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 30, 30, 11, 6, 11, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 41, 41, 23, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 6, 23, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [11, 49, 39, 8, 9, 10, 7, 12, 46, 47, 48, 40, 24, 41, 23, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082774 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082774 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082774/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082774 Building REAL300000082775 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082775' /scratch/stefan/7930160/working/building/REAL300000082775 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082775 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082775/0 /scratch/stefan/7930160/working/building/REAL300000082775 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/836 `/scratch/stefan/7930160/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C)=N1) `REAL300000082775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082775 none COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 133, 133, 133, 133, 131, 57, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 135, 135, 135, 133, 133, 133, 133, 57, 13, 1, 1, 1, 133, 133, 133] 135 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082775 none COC1=CC(C)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 1, 9, 9, 61, 133, 133, 133, 133, 133, 133, 135, 135, 133, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 9, 61, 133, 133, 133, 2, 2, 2] 135 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082775 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082775 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082775/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082775 Building REAL300000082776 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082776' /scratch/stefan/7930160/working/building/REAL300000082776 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082776 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082776/0 /scratch/stefan/7930160/working/building/REAL300000082776 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/837 `/scratch/stefan/7930160/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O) `REAL300000082776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082776 none COC1=CC(Cl)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 238 conformations in input total number of sets (complete confs): 238 using faster count positions algorithm for large data unique positions, atoms: [119, 98, 98, 98, 98, 98, 98, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 98, 98, 119, 119, 119, 98, 98, 56, 11, 1, 1, 1, 196] 238 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 386 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082776 none COC1=CC(Cl)=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 238 conformations in input total number of sets (complete confs): 238 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 98, 98, 98, 98, 98, 98, 119, 119, 98, 1, 1, 4, 4, 4, 1, 1, 10, 40, 98, 98, 98, 2] 238 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 267 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082776 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082776 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082776/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082776 Building REAL300000082777 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082777' /scratch/stefan/7930160/working/building/REAL300000082777 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082777 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082777/0 /scratch/stefan/7930160/working/building/REAL300000082777 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/838 `/scratch/stefan/7930160/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1) `REAL300000082777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082777 none COC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 52, 52, 52, 30, 30, 30, 30, 30, 30, 1, 1, 1, 30, 30, 30, 30, 30] 52 rigid atoms, others: [36, 37, 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, 35, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082777 none COC1=CC=C2NC3=C(CC(N=NC4=CC=C(F)C(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 30, 30, 30, 52, 52, 30, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 30, 30, 30, 1, 1, 1, 1, 1] 52 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43] set([0, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082777 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082777 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082777/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082777 Building REAL300000082778 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082778' /scratch/stefan/7930160/working/building/REAL300000082778 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082778 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082778/0 /scratch/stefan/7930160/working/building/REAL300000082778 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/839 `/scratch/stefan/7930160/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-]) `REAL300000082778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082778 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082778 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [32, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 37, 37, 37, 37, 37, 37, 37, 37, 33, 33, 33, 9, 1, 1, 1, 37, 37] 37 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082778 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082778/1 /scratch/stefan/7930160/working/building/REAL300000082778 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/840 `/scratch/stefan/7930160/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O) `REAL300000082778.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082778 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 254 conformations in input total number of sets (complete confs): 254 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 55, 127, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 127, 127, 127, 1, 1, 2] 254 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 235 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: REAL300000082778 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 254 conformations in input total number of sets (complete confs): 254 using faster count positions algorithm for large data unique positions, atoms: [43, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 127, 127, 127, 127, 127, 127, 127, 127, 44, 44, 44, 11, 1, 1, 1, 127, 127, 254] 254 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 445 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082778 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082778 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082778/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082778/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082778 Building REAL300000082779 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082779' /scratch/stefan/7930160/working/building/REAL300000082779 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082779 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082779/0 /scratch/stefan/7930160/working/building/REAL300000082779 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/841 `/scratch/stefan/7930160/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=CC=C1F) `REAL300000082779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082779 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 33, 9, 1, 1, 1, 1, 1, 1, 62, 62] 62 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082779 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 43, 43, 62, 62, 62, 61, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 10, 43, 62, 61, 62, 62, 62, 62, 1, 1] 62 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082779 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082779 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082779/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082779 Building REAL300000082780 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082780' /scratch/stefan/7930160/working/building/REAL300000082780 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082780 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082780/0 /scratch/stefan/7930160/working/building/REAL300000082780 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/842 `/scratch/stefan/7930160/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(Cl)=C1) `REAL300000082780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082780 none O=C([O-])C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 24, 27, 27, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 27, 27, 27, 27, 22, 5, 1, 1, 1, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082780 none O=C([O-])C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 6, 20, 27, 27, 27, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082780 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082780 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082780/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082780 Building REAL300000082781 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082781' /scratch/stefan/7930160/working/building/REAL300000082781 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082781 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082781/0 /scratch/stefan/7930160/working/building/REAL300000082781 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/843 `/scratch/stefan/7930160/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CN2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CN=C12) `REAL300000082781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082781 none CC1=CC(Br)=CN2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 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, 4, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 162, 162, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 162, 162, 162, 163, 163, 163, 162, 162, 66, 12, 1, 1, 1, 162] 163 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082781 none CC1=CC(Br)=CN2C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 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, 4, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 80, 162, 162, 162, 162, 162, 162, 163, 163, 162, 1, 1, 1, 2, 2, 2, 1, 1, 12, 80, 162, 162, 162, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 27, 28] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082781 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082781 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082781/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082781 Building REAL300000082782 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082782' /scratch/stefan/7930160/working/building/REAL300000082782 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082782 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082782/0 /scratch/stefan/7930160/working/building/REAL300000082782 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/844 `/scratch/stefan/7930160/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F) `REAL300000082782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 28, 40, 28, 28, 13, 4, 4, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 1, 1, 28, 28, 28, 28, 28, 13, 4, 1, 8, 8, 31, 31, 31, 31, 28, 28] 201 rigid atoms, others: [8, 9, 10, 11, 12, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 25, 25, 28, 28, 28, 85, 201, 201, 201, 201, 201, 28, 28, 1, 1, 1, 1, 1, 7, 25, 28, 85, 85, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 101, 40, 40, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 101, 40, 31, 7, 7, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 404 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082782 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082782/1 /scratch/stefan/7930160/working/building/REAL300000082782 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/845 `/scratch/stefan/7930160/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F) `REAL300000082782.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 52, 75, 52, 52, 34, 34, 6, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 1, 1, 52, 52, 52, 52, 52, 6, 6, 1, 7, 7, 21, 21, 21, 21, 52, 52] 201 rigid atoms, others: [8, 9, 10, 11, 12, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 24, 52, 52, 52, 121, 201, 201, 201, 201, 201, 52, 52, 1, 1, 1, 1, 1, 24, 24, 52, 121, 121, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082782 none O=C([O-])C1=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 167, 52, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 52, 52, 21, 7, 7, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082782 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082782 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082782/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082782/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082782 Building REAL300000082783 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082783' /scratch/stefan/7930160/working/building/REAL300000082783 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082783 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082783/0 /scratch/stefan/7930160/working/building/REAL300000082783 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/846 `/scratch/stefan/7930160/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1F) `REAL300000082783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082783 none O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 38, 38, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082783 none O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 1, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082783 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082783 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082783/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082783 Building REAL300000082784 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082784' /scratch/stefan/7930160/working/building/REAL300000082784 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082784 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082784/0 /scratch/stefan/7930160/working/building/REAL300000082784 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/847 `/scratch/stefan/7930160/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC2=CC=CN=C12) `REAL300000082784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082784 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 49, 11, 1, 1, 1, 122, 122, 122, 122] 122 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082784 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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, 10, 10, 56, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 56, 122, 122, 122, 1, 1, 1, 1] 122 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 17, 18, 19, 20, 21, 22, 23, 36, 27] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082784 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082784 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082784/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082784 Building REAL300000082785 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082785' /scratch/stefan/7930160/working/building/REAL300000082785 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082785 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082785/0 /scratch/stefan/7930160/working/building/REAL300000082785 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/848 `/scratch/stefan/7930160/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1) `REAL300000082785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082785 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 61, 12, 1, 1, 1, 160, 160, 160, 160] 160 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082785 none CC1=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 71, 160, 160, 160, 160, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 71, 160, 160, 160, 1, 1, 1, 1] 160 rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082785 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082785 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082785/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082785 Building REAL300000082786 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082786' /scratch/stefan/7930160/working/building/REAL300000082786 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082786 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082786/0 /scratch/stefan/7930160/working/building/REAL300000082786 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/849 `/scratch/stefan/7930160/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082786 none COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 124, 201, 76, 27, 27, 41, 41, 15, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 201, 201, 201, 121, 121, 41, 40, 14, 4, 1, 1, 1, 41, 41] 201 rigid atoms, others: [34, 35, 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, 33, 37, 38]) total number of confs: 677 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: REAL300000082786 none COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [60, 60, 11, 60, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 40, 40, 40, 40, 40, 41, 60, 60, 40, 1, 1, 61, 60, 60, 11, 11, 1, 1, 6, 20, 40, 40, 40, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 24, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082786 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082786 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082786/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082786 Building REAL300000082787 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082787' /scratch/stefan/7930160/working/building/REAL300000082787 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082787 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082787/0 /scratch/stefan/7930160/working/building/REAL300000082787 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/850 `/scratch/stefan/7930160/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C)(C)C1) `REAL300000082787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082787 none CC1(C)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 58 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: REAL300000082787 none CC1(C)CC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 25, 25, 25, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 42, 43, 34, 17, 18, 35, 20, 21, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082787 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082787 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082787/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082787 Building REAL300000082788 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082788' /scratch/stefan/7930160/working/building/REAL300000082788 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082788 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082788/0 /scratch/stefan/7930160/working/building/REAL300000082788 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/851 `/scratch/stefan/7930160/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000082788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082788 none CC(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 164, 108, 177, 177, 54, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 177, 177, 201, 201, 201, 201, 177, 177, 55, 55, 55, 12, 1, 1, 1, 177, 177] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 661 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082788 none CC(=O)NC1=CC=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 67, 177, 177, 177, 177, 177, 177, 192, 192, 177, 1, 1, 3, 3, 3, 3, 1, 1, 13, 13, 13, 67, 177, 177, 177, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 38, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 379 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082788 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082788 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082788/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082788 Building REAL300000082789 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082789' /scratch/stefan/7930160/working/building/REAL300000082789 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082789 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082789/0 /scratch/stefan/7930160/working/building/REAL300000082789 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/852 `/scratch/stefan/7930160/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Cl) `REAL300000082789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082789 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 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 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, 48, 48, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 112, 112, 84, 112, 112, 112, 112, 112, 48, 13, 1, 1, 1, 112, 112] 112 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082789 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 56, 112, 112, 111, 111, 112, 112, 112, 112, 112, 1, 1, 1, 1, 2, 2, 2, 1, 8, 56, 112, 112, 112, 1, 1] 112 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 24, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082789 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082789 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082789/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082789 Building REAL300000082790 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082790' /scratch/stefan/7930160/working/building/REAL300000082790 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082790 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082790/0 /scratch/stefan/7930160/working/building/REAL300000082790 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/853 `/scratch/stefan/7930160/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1F) `REAL300000082790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082790 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 60, 74, 60, 60, 30, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 2, 13, 13, 13, 13, 13, 13, 1, 60, 60, 60, 60, 60, 30, 7, 1, 1, 13, 13, 10, 13, 60, 60] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 23, 31] 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, 33, 34, 35, 36, 37, 38]) 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: REAL300000082790 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 9, 36, 36, 60, 60, 60, 60, 201, 201, 156, 201, 201, 201, 201, 201, 201, 60, 1, 1, 1, 1, 1, 9, 36, 60, 60, 201, 201, 198, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 27, 24, 25, 26, 38, 28, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082790 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 128, 51, 51, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 128, 50, 13, 13, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 420 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082790 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082790 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082790/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082790 Building REAL300000082791 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082791' /scratch/stefan/7930160/working/building/REAL300000082791 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082791 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082791/0 /scratch/stefan/7930160/working/building/REAL300000082791 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/854 `/scratch/stefan/7930160/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=CC=C1F) `REAL300000082791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082791 none O=C([O-])C1=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 80, 71, 71, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 71, 71, 70, 70, 71, 34, 9, 1, 1, 4, 4, 1, 4, 4, 71, 71] 80 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000082791 none O=C([O-])C1=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 29, 29, 71, 71, 71, 71, 71, 80, 80, 71, 80, 80, 1, 1, 1, 1, 1, 11, 29, 71, 71, 80, 80, 71, 80, 80, 1, 1] 80 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082791 none O=C([O-])C1=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 48, 20, 20, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 48, 20, 4, 4, 1, 1, 1, 1, 1, 80, 80] 80 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 173 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082791 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082791 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082791/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082791 Building REAL300000082792 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082792' /scratch/stefan/7930160/working/building/REAL300000082792 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082792 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082792/0 /scratch/stefan/7930160/working/building/REAL300000082792 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/855 `/scratch/stefan/7930160/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082792 none CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 60, 160, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 60, 60, 60, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1] 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]) total number of confs: 680 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: REAL300000082792 none CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 37, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40]) total number of confs: 331 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082792 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082792/1 /scratch/stefan/7930160/working/building/REAL300000082792 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/856 `/scratch/stefan/7930160/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082792.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082792 none CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 8, 41, 88, 111, 111, 111, 111, 111, 111, 111, 111, 111, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 41, 41, 41, 88, 88, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1] 111 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 436 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: REAL300000082792 none CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 79, 79, 111, 111, 111, 111, 111, 111, 111, 111, 111, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111] 111 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 36, 38, 37, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082792 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082792 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082792/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082792/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082792 Building REAL300000082793 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082793' /scratch/stefan/7930160/working/building/REAL300000082793 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082793 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082793/0 /scratch/stefan/7930160/working/building/REAL300000082793 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/857 `/scratch/stefan/7930160/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(C3=CC=CC(C(F)(F)F)=C3)CC2)=CC=C1F) `REAL300000082793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082793 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=CC(C(F)(F)F)=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 43, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 12, 12, 12, 1, 1, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 1, 1, 1, 1, 27, 27] 153 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 40, 42, 41, 22, 23, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 35, 36, 37, 38, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082793 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=CC(C(F)(F)F)=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 153, 153, 50, 153, 153, 153, 153, 153, 153, 27, 27, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 153, 153, 57, 153, 27, 27, 27, 27, 1, 1] 153 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082793 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=CC(C(F)(F)F)=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 153, 66, 66, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 153, 153, 153, 153, 153, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12, 153, 153] 153 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082793 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082793 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082793/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082793 Building REAL300000082794 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082794' /scratch/stefan/7930160/working/building/REAL300000082794 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082794 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082794/0 /scratch/stefan/7930160/working/building/REAL300000082794 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/858 `/scratch/stefan/7930160/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082794 none CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 46, 61, 46, 46, 46, 46, 46, 46, 46, 45, 46, 46, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 61, 61, 61, 61, 61, 46, 46, 46, 46, 13, 1, 1, 1] 61 rigid atoms, others: [36, 37, 38, 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]) 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: REAL300000082794 none CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 46, 46, 45, 45, 46, 46, 61, 61, 46, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 46, 46, 46] 61 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 33, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082794 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082794 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082794/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082794 Building REAL300000082795 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082795' /scratch/stefan/7930160/working/building/REAL300000082795 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082795 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082795/0 /scratch/stefan/7930160/working/building/REAL300000082795 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/859 `/scratch/stefan/7930160/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)N(C)C2=C1) `REAL300000082795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082795 none CN(C)C1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)N(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 64, 46, 46, 46, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 46, 46, 46, 46, 46, 64, 64, 64, 64, 64, 64, 46, 46, 12, 1, 1, 1, 47, 47, 47, 46] 64 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082795 none CN(C)C1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)N(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 46, 46, 46, 46, 46, 46, 64, 64, 46, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 46, 46, 46, 2, 2, 2, 1] 64 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 8, 9, 41, 7, 20, 21, 22, 23, 24, 25] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 34, 35, 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/7930160/working/building/REAL300000082795 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082795 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082795/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082795 Building REAL300000082796 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082796' /scratch/stefan/7930160/working/building/REAL300000082796 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082796 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082796/0 /scratch/stefan/7930160/working/building/REAL300000082796 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/860 `/scratch/stefan/7930160/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)S2)=CC=C1F) `REAL300000082796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082796 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 91, 41, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 92, 92, 92, 92, 91, 41, 6, 1, 1, 92, 92] 92 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 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: REAL300000082796 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 54, 54, 91, 91, 91, 91, 92, 92, 92, 91, 1, 1, 1, 1, 1, 12, 54, 91, 91, 1, 1] 92 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082796 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082796 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082796/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082796 Building REAL300000082797 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082797' /scratch/stefan/7930160/working/building/REAL300000082797 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082797 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082797/0 /scratch/stefan/7930160/working/building/REAL300000082797 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/861 `/scratch/stefan/7930160/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=N1) `REAL300000082797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082797 none CC(C)(C)N1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 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, 4, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 64, 102, 102, 64, 64, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 64, 64, 102, 102, 102, 102, 102, 102, 102, 102, 102, 64, 47, 11, 1, 1, 1] 102 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082797 none CC(C)(C)N1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 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, 4, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 7, 7, 31, 64, 64, 64, 64, 64, 64, 79, 79, 64, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 31, 64, 64, 64] 102 rigid atoms, others: [1, 4, 5, 6, 7, 20, 21, 31] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082797 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082797/1 /scratch/stefan/7930160/working/building/REAL300000082797 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/862 `/scratch/stefan/7930160/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1) `REAL300000082797.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082797 none CC(C)(C)N1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 201, 201, 135, 135, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 46, 46, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082797 none CC(C)(C)N1C=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 9, 61, 61, 135, 135, 135, 135, 135, 135, 177, 177, 135, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 9, 9, 135, 135, 135] 201 rigid atoms, others: [1, 4, 5, 6, 7, 20, 21, 31] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082797 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082797 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082797/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082797/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082797 Building REAL300000082798 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082798' /scratch/stefan/7930160/working/building/REAL300000082798 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082798 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082798/0 /scratch/stefan/7930160/working/building/REAL300000082798 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/863 `/scratch/stefan/7930160/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=CC=C1F) `REAL300000082798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082798 none O=C([O-])C1=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 84, 84, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 39, 10, 1, 1, 1, 1, 84, 84] 84 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000082798 none O=C([O-])C1=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 46, 46, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 11, 46, 84, 84, 84, 84, 1, 1] 84 rigid atoms, others: [32, 1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082798 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082798 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082798/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082798 Building REAL300000082799 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082799' /scratch/stefan/7930160/working/building/REAL300000082799 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082799 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082799/0 /scratch/stefan/7930160/working/building/REAL300000082799 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/864 `/scratch/stefan/7930160/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=CC=C1F) `REAL300000082799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082799 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 70, 111, 70, 70, 33, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 13, 1, 70, 70, 70, 70, 70, 33, 7, 1, 1, 13, 13, 13, 70, 70] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082799 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 42, 42, 70, 70, 70, 70, 201, 201, 201, 201, 201, 201, 192, 70, 1, 1, 1, 1, 1, 9, 42, 70, 70, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082799 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 143, 46, 46, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 143, 46, 13, 13, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 456 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082799 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082799 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082799/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082799 Building REAL300000082800 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082800' /scratch/stefan/7930160/working/building/REAL300000082800 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082800 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082800/0 /scratch/stefan/7930160/working/building/REAL300000082800 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/865 `/scratch/stefan/7930160/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000082800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082800 none CC(C)(C)OC(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 134, 135, 135, 120, 82, 120, 29, 4, 1, 4, 4, 12, 26, 26, 26, 26, 26, 26, 36, 36, 26, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 135, 135, 82, 29, 29, 12, 26, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [9, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082800 none CC(C)(C)OC(=O)NCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 186, 148, 186, 74, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 15, 26, 26, 15, 26, 26, 200, 200, 200, 200, 200, 200, 200, 200, 200, 148, 74, 74, 5, 1, 1, 1, 26, 26, 15, 26, 26] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082800 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082800 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082800/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082800 Building REAL300000082801 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082801' /scratch/stefan/7930160/working/building/REAL300000082801 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082801 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082801/0 /scratch/stefan/7930160/working/building/REAL300000082801 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/866 `/scratch/stefan/7930160/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082801 none CCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 147, 53, 147, 53, 53, 53, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 53, 201, 201, 201, 201, 201, 147, 147, 147, 53, 53, 22, 6, 1, 1, 1, 53] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 657 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: REAL300000082801 none CCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 27, 53, 53, 53, 53, 53, 53, 79, 79, 53, 1, 1, 29, 29, 29, 29, 29, 10, 10, 10, 1, 1, 7, 27, 53, 53, 53, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 21, 22, 38, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 312 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082801 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082801 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082801/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082801 Building REAL300000082802 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082802' /scratch/stefan/7930160/working/building/REAL300000082802 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082802 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082802/0 /scratch/stefan/7930160/working/building/REAL300000082802 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/867 `/scratch/stefan/7930160/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)OC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082802 none CN1C(=O)OC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 115, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 115, 115, 115, 116, 116, 116, 115, 57, 11, 1, 1, 1, 115, 115] 116 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082802 none CN1C(=O)OC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 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 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, 10, 10, 53, 115, 115, 115, 115, 115, 115, 116, 116, 115, 1, 1, 1, 2, 2, 2, 1, 10, 53, 115, 115, 115, 1, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 33, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 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/7930160/working/building/REAL300000082802 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082802 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082802/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082802 Building REAL300000082803 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082803' /scratch/stefan/7930160/working/building/REAL300000082803 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082803 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082803/0 /scratch/stefan/7930160/working/building/REAL300000082803 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/868 `/scratch/stefan/7930160/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082803 none CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [32, 7, 32, 86, 148, 148, 148, 148, 148, 148, 148, 148, 148, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 32, 32, 86, 86, 148, 148, 148, 148, 148, 148, 1, 1, 1] 148 rigid atoms, others: [37, 38, 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, 36]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082803 none CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 90, 90, 148, 148, 148, 148, 148, 148, 148, 148, 148, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 148, 148, 148] 148 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 36, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082803 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082803 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082803/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082803 Building REAL300000082804 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082804' /scratch/stefan/7930160/working/building/REAL300000082804 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082804 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082804/0 /scratch/stefan/7930160/working/building/REAL300000082804 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/869 `/scratch/stefan/7930160/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C2) `REAL300000082804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082804 none COC1=CC=CC2=C1CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 43, 43, 43, 43, 43, 43, 43, 43, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 54, 54, 54, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 43, 43] 54 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: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082804 none COC1=CC=CC2=C1CCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 43, 43, 43, 43, 43, 43, 54, 54, 43, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 1, 1] 54 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39] set([0, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082804 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082804 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082804/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082804 Building REAL300000082805 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082805' /scratch/stefan/7930160/working/building/REAL300000082805 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082805 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082805/0 /scratch/stefan/7930160/working/building/REAL300000082805 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/870 `/scratch/stefan/7930160/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3OCCO3)S2)=CC=C1F) `REAL300000082805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082805 none O=C([O-])C1=CC(NN=CC2=CN=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 71, 102, 71, 71, 39, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 71, 71, 71, 71, 71, 39, 6, 1, 13, 13, 13, 13, 13, 71, 71] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000082805 none O=C([O-])C1=CC(NN=CC2=CN=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 8, 32, 32, 71, 71, 71, 71, 201, 201, 201, 201, 71, 1, 1, 1, 1, 1, 8, 32, 71, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082805 none O=C([O-])C1=CC(NN=CC2=CN=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 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, 53, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 167, 53, 13, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 475 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082805 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082805 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082805/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082805 Building REAL300000082806 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082806' /scratch/stefan/7930160/working/building/REAL300000082806 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082806 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082806/0 /scratch/stefan/7930160/working/building/REAL300000082806 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/871 `/scratch/stefan/7930160/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=CC=C1F) `REAL300000082806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082806 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 135, 160, 135, 135, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 135, 135, 135, 135, 135, 67, 11, 1, 1, 6, 6, 6, 6, 6, 135, 135] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000082806 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 36, 36, 135, 135, 135, 42, 135, 135, 201, 201, 201, 201, 135, 135, 1, 1, 1, 1, 1, 8, 36, 135, 63, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 25, 22, 23, 24, 36, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082806 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 137, 46, 46, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 137, 46, 6, 6, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082806 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082806 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082806/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082806 Building REAL300000082807 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082807' /scratch/stefan/7930160/working/building/REAL300000082807 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082807 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082807/0 /scratch/stefan/7930160/working/building/REAL300000082807 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/872 `/scratch/stefan/7930160/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=CC=C1F) `REAL300000082807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082807 none O=C([O-])C1=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 200, 200, 70, 70, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 8, 8, 1, 1, 1, 200, 200] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082807 none O=C([O-])C1=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 42, 200, 200, 200, 200, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 42, 42, 200, 200, 200, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082807 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082807/1 /scratch/stefan/7930160/working/building/REAL300000082807 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/873 `/scratch/stefan/7930160/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=CC=C1F) `REAL300000082807.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082807 none O=C([O-])C1=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 70, 70, 71, 41, 6, 1, 1, 1, 71, 71] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000082807 none O=C([O-])C1=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 45, 45, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 13, 45, 71, 71, 71, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082807 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082807 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082807/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082807/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082807 Building REAL300000082808 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082808' /scratch/stefan/7930160/working/building/REAL300000082808 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082808 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082808/0 /scratch/stefan/7930160/working/building/REAL300000082808 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/874 `/scratch/stefan/7930160/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=CC=C1F) `REAL300000082808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082808 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 38, 56, 38, 38, 14, 3, 3, 1, 1, 1, 1, 1, 1, 6, 19, 58, 58, 1, 1, 38, 38, 38, 38, 38, 13, 3, 1, 1, 19, 19, 58, 58, 58, 58, 58, 1, 1, 38, 38] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 306 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: REAL300000082808 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 38, 38, 27, 27, 93, 130, 201, 201, 38, 38, 1, 1, 1, 1, 1, 7, 27, 38, 38, 130, 130, 201, 201, 201, 201, 201, 38, 38, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 622 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082808 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 158, 93, 93, 51, 32, 58, 58, 32, 10, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 158, 93, 58, 58, 10, 10, 1, 1, 1, 1, 1, 58, 58, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 608 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082808 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082808 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082808/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082808 Building REAL300000082809 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082809' /scratch/stefan/7930160/working/building/REAL300000082809 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082809 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082809/0 /scratch/stefan/7930160/working/building/REAL300000082809 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/875 `/scratch/stefan/7930160/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CCC2=C1OC) `REAL300000082809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082809 none COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CCC2=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [130, 58, 58, 58, 58, 58, 58, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 58, 58, 58, 58, 112, 130, 130, 130, 58, 58, 10, 1, 1, 1, 58, 58, 58, 58, 112, 112, 112] 134 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 302 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: REAL300000082809 none COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CCC2=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 58, 58, 58, 58, 58, 58, 88, 88, 58, 1, 1, 1, 1, 1, 6, 3, 3, 3, 1, 1, 9, 58, 58, 58, 1, 1, 1, 1, 6, 6, 6] 134 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 37, 19, 20, 21, 22, 23, 36, 28, 29, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082809 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082809 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082809/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082809 Building REAL300000082810 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082810' /scratch/stefan/7930160/working/building/REAL300000082810 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082810 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082810/0 /scratch/stefan/7930160/working/building/REAL300000082810 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/876 `/scratch/stefan/7930160/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(F)C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl) `REAL300000082810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082810 none N#CC1=C(F)C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 78, 78, 78, 45, 10, 1, 1, 1] 78 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082810 none N#CC1=C(F)C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 10, 36, 78, 78, 78] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082810 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082810 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082810/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082810 Building REAL300000082811 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082811' /scratch/stefan/7930160/working/building/REAL300000082811 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082811 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082811/0 /scratch/stefan/7930160/working/building/REAL300000082811 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/877 `/scratch/stefan/7930160/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C=C(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)OC2=C1) `REAL300000082811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082811 none CC1=CC=C2C=C(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 37, 7, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 37, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082811 none CC1=CC=C2C=C(C(C)N=NC3=CC=C(F)C(C(=O)[O-])=C3)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082811 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082811/1 /scratch/stefan/7930160/working/building/REAL300000082811 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/878 `/scratch/stefan/7930160/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1) `REAL300000082811.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082811 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 32, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 63, 63, 62, 1, 1, 1, 2, 2, 2, 1] 63 rigid atoms, others: [32, 1, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082811 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 62, 62, 62, 62, 62, 63, 63, 62, 62, 37, 37, 37, 10, 1, 1, 1, 62, 62, 62, 63, 63, 63, 63] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082811 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082811 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082811/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082811/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082811 Building REAL300000082812 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082812' /scratch/stefan/7930160/working/building/REAL300000082812 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082812 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082812/0 /scratch/stefan/7930160/working/building/REAL300000082812 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/879 `/scratch/stefan/7930160/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=C(Cl)S2)=CC=C1F) `REAL300000082812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082812 none O=C([O-])C1=CC(NN=CC2=CC(Br)=C(Cl)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 16, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 50, 6, 1, 93, 93] 93 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 24, 25]) 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: REAL300000082812 none O=C([O-])C1=CC(NN=CC2=CC(Br)=C(Cl)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 16, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 47, 47, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 13, 47, 93, 1, 1] 93 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082812 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082812 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082812/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082812 Building REAL300000082813 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082813' /scratch/stefan/7930160/working/building/REAL300000082813 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082813 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082813/0 /scratch/stefan/7930160/working/building/REAL300000082813 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/880 `/scratch/stefan/7930160/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=CC=C1F) `REAL300000082813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082813 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 36, 10, 1, 1, 67, 67] 67 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082813 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 42, 42, 67, 67, 62, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 12, 42, 67, 67, 1, 1] 67 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082813 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082813 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082813/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082813 Building REAL300000082814 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082814' /scratch/stefan/7930160/working/building/REAL300000082814 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082814 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082814/0 /scratch/stefan/7930160/working/building/REAL300000082814 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/881 `/scratch/stefan/7930160/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CSC(Cl)=C2Cl)=CC=C1F) `REAL300000082814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082814 none O=C([O-])C1=CC(NN=CC2=CSC(Cl)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 45, 9, 1, 74, 74] 74 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 24, 25]) 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: REAL300000082814 none O=C([O-])C1=CC(NN=CC2=CSC(Cl)=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 16, 1, 16, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 48, 48, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 12, 48, 74, 1, 1] 74 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082814 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082814 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082814/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082814 Building REAL300000082815 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082815' /scratch/stefan/7930160/working/building/REAL300000082815 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082815 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082815/0 /scratch/stefan/7930160/working/building/REAL300000082815 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/882 `/scratch/stefan/7930160/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082815 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 33, 33, 78, 78, 78, 78, 78, 78, 78, 78, 78, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 78, 78, 78, 6, 6] 78 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082815 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1, 12, 12, 47, 47, 47, 47, 47, 47, 51, 51, 47, 1, 2, 2, 2, 6, 6, 3, 6, 6, 1, 1, 1, 1, 1, 47, 47, 47, 1, 1] 78 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 8, 9, 10, 11, 34, 40, 41, 23] set([3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082815 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 78, 78, 75, 78, 78, 47, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 47, 47, 47, 78, 78, 75, 78, 78, 47, 47, 47, 47, 47, 1, 1, 1, 47, 47] 78 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40, 41]) total number of confs: 176 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082815 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082815 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082815/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082815 Building REAL300000082816 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082816' /scratch/stefan/7930160/working/building/REAL300000082816 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082816 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082816/0 /scratch/stefan/7930160/working/building/REAL300000082816 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/883 `/scratch/stefan/7930160/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=CC=C1F) `REAL300000082816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082816 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 66, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 155, 155, 155, 155, 155, 66, 12, 1, 1, 1, 155, 155] 155 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000082816 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 59, 59, 155, 155, 155, 105, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 13, 59, 155, 155, 155, 1, 1] 155 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: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082816 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082816 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082816/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082816 Building REAL300000082817 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082817' /scratch/stefan/7930160/working/building/REAL300000082817 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082817 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082817/0 /scratch/stefan/7930160/working/building/REAL300000082817 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/884 `/scratch/stefan/7930160/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082817 none CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 53, 53, 96, 96, 96, 96, 96, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 96, 96, 96, 96, 96, 96, 53, 13, 1, 1, 1] 96 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 448 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082817 none CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 2, 2, 2, 1, 1, 1, 1, 10, 10, 46, 96, 96, 96, 96, 96, 96, 96, 96, 96, 2, 2, 2, 1, 1, 1, 10, 46, 96, 96, 96] 96 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 27, 28, 29] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082817 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082817 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082817/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082817 Building REAL300000082818 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082818' /scratch/stefan/7930160/working/building/REAL300000082818 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082818 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082818/0 /scratch/stefan/7930160/working/building/REAL300000082818 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/885 `/scratch/stefan/7930160/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(Cl)=N1) `REAL300000082818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082818 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 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, 46, 46, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 120, 120, 120, 113, 120, 120, 120, 120, 46, 13, 1, 1, 1, 120] 120 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) 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: REAL300000082818 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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 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, 10, 10, 63, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 2, 2, 2, 1, 10, 63, 120, 120, 120, 1] 120 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082818 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082818 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082818/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082818 Building REAL300000082819 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082819' /scratch/stefan/7930160/working/building/REAL300000082819 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082819 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082819/0 /scratch/stefan/7930160/working/building/REAL300000082819 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/886 `/scratch/stefan/7930160/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1F) `REAL300000082819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082819 none O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 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, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 53, 10, 1, 1, 1, 1, 1, 1, 122, 122] 122 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082819 none O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 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: [3, 1, 3, 1, 1, 1, 1, 13, 55, 55, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 13, 55, 122, 122, 122, 122, 122, 122, 1, 1] 122 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082819 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082819 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082819/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082819 Building REAL300000082820 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082820' /scratch/stefan/7930160/working/building/REAL300000082820 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082820 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082820/0 /scratch/stefan/7930160/working/building/REAL300000082820 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/887 `/scratch/stefan/7930160/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082820 none NC(=O)C1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 145, 166, 145, 145, 145, 145, 145, 71, 71, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 166, 166, 145, 145, 145, 145, 71, 13, 1, 1, 1] 166 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082820 none NC(=O)C1=CC=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 59, 145, 145, 145, 145, 145, 145, 152, 152, 145, 4, 4, 1, 1, 1, 1, 11, 59, 145, 145, 145] 166 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 32, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082820 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082820 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082820/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082820 Building REAL300000082821 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082821' /scratch/stefan/7930160/working/building/REAL300000082821 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082821 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082821/0 /scratch/stefan/7930160/working/building/REAL300000082821 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/888 `/scratch/stefan/7930160/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2N=C(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1) `REAL300000082821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082821 none COC1=CC=C2N=C(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 128, 129, 129, 129, 129, 129, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 129, 129, 129, 201, 201, 201, 129, 129, 30, 30, 1, 1, 1, 129] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082821 none COC1=CC=C2N=C(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 9, 60, 60, 129, 129, 129, 129, 129, 129, 201, 201, 129, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 129, 129, 129, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082821 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082821/1 /scratch/stefan/7930160/working/building/REAL300000082821 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/889 `/scratch/stefan/7930160/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2N=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1) `REAL300000082821.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082821 none COC1=CC=C2N=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 94, 94, 94, 94, 94, 94, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 94, 94, 94, 129, 129, 129, 94, 94, 49, 11, 1, 1, 1, 94] 129 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082821 none COC1=CC=C2N=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 94, 94, 94, 94, 94, 94, 129, 129, 94, 1, 1, 1, 3, 3, 3, 1, 1, 9, 47, 94, 94, 94, 1] 129 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082821 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082821 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082821/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082821/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082821 Building REAL300000082822 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082822' /scratch/stefan/7930160/working/building/REAL300000082822 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082822 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082822/0 /scratch/stefan/7930160/working/building/REAL300000082822 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/890 `/scratch/stefan/7930160/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=NC=C2[N+](=O)[O-])=CC=C1F) `REAL300000082822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082822 none O=C([O-])C1=CC(NN=CC2=CC=NC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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, 43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 94, 94, 94, 94, 94, 43, 7, 1, 1, 1, 94, 94] 94 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) 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: REAL300000082822 none O=C([O-])C1=CC(NN=CC2=CC=NC=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.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, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 13, 62, 62, 94, 94, 76, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 13, 62, 94, 94, 94, 1, 1] 94 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082822 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082822 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082822/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082822 Building REAL300000082823 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082823' /scratch/stefan/7930160/working/building/REAL300000082823 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082823 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082823/0 /scratch/stefan/7930160/working/building/REAL300000082823 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/891 `/scratch/stefan/7930160/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2C=C1) `REAL300000082823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082823 none CC1=NC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 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, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 118, 118, 118, 118, 118, 118, 118, 118, 53, 13, 1, 1, 1, 118, 118, 118] 118 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082823 none CC1=NC2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 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, 10, 10, 52, 118, 118, 117, 117, 118, 118, 118, 118, 118, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 52, 118, 118, 118, 1, 1, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23, 36, 27, 28] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082823 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082823 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082823/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082823 Building REAL300000082824 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082824' /scratch/stefan/7930160/working/building/REAL300000082824 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082824 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082824/0 /scratch/stefan/7930160/working/building/REAL300000082824 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/892 `/scratch/stefan/7930160/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(Cl)=C1) `REAL300000082824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082824 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 72, 169, 169, 169, 169, 169, 169, 169, 169, 169, 1, 1, 1, 1, 1, 1, 13, 13, 13, 72, 169, 169, 169, 1, 1] 169 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 306 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082824 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 169, 169, 169, 169, 169, 55, 55, 55, 11, 1, 1, 1, 169, 169] 169 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 24, 25, 26] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082824 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082824 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082824/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082824 Building REAL300000082825 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082825' /scratch/stefan/7930160/working/building/REAL300000082825 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082825 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082825/0 /scratch/stefan/7930160/working/building/REAL300000082825 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/893 `/scratch/stefan/7930160/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2SCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1) `REAL300000082825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082825 none COC1=CC=C2SCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 42, 69, 69, 69, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 42] 69 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 123 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: REAL300000082825 none COC1=CC=C2SCCC(=NNC3=CC=C(F)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 42, 42, 42, 69, 69, 42, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 1] 69 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 22, 23, 27, 28, 29, 30, 31] set([0, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 176 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082825 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082825 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082825/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082825 Building REAL300000082826 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082826' /scratch/stefan/7930160/working/building/REAL300000082826 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082826 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082826/0 /scratch/stefan/7930160/working/building/REAL300000082826 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/894 `/scratch/stefan/7930160/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCCCC1) `REAL300000082826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082826 none COCCC1(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [201, 137, 137, 83, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 95, 95, 85, 95, 95, 201, 201, 201, 139, 139, 130, 130, 34, 34, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 713 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082826 none COCCC1(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [22, 10, 10, 1, 1, 1, 7, 33, 33, 95, 95, 95, 95, 95, 95, 131, 131, 95, 1, 1, 1, 1, 1, 22, 22, 22, 10, 10, 10, 10, 7, 7, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 3, 4, 5, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 335 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082826 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082826 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082826/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082826 Building REAL300000082827 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082827' /scratch/stefan/7930160/working/building/REAL300000082827 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082827 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082827/0 /scratch/stefan/7930160/working/building/REAL300000082827 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/895 `/scratch/stefan/7930160/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC(O)=CC=C32)=CC=C1F) `REAL300000082827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082827 none O=C([O-])C1=CC(NN=C2CCC3=CC(O)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 1, 2, 1, 1, 28, 28] 56 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 33, 29]) total number of confs: 41 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082827 none O=C([O-])C1=CC(NN=C2CCC3=CC(O)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 56, 28, 28, 1, 1] 56 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082827 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082827 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082827/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082827 Building REAL300000082828 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082828' /scratch/stefan/7930160/working/building/REAL300000082828 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082828 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082828/0 /scratch/stefan/7930160/working/building/REAL300000082828 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/896 `/scratch/stefan/7930160/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=C(F)C=CC=C3N2)=CC=C1F) `REAL300000082828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082828 none O=C([O-])C1=CC(NN=CC2=CC3=C(F)C=CC=C3N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 64, 27, 6, 1, 1, 1, 1, 1, 65, 65] 65 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082828 none O=C([O-])C1=CC(NN=CC2=CC3=C(F)C=CC=C3N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 48, 48, 64, 64, 64, 65, 64, 64, 64, 64, 42, 1, 1, 1, 1, 1, 10, 48, 65, 64, 64, 64, 64, 1, 1] 65 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082828 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082828 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082828/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082828 Building REAL300000082829 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082829' /scratch/stefan/7930160/working/building/REAL300000082829 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082829 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082829/0 /scratch/stefan/7930160/working/building/REAL300000082829 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/897 `/scratch/stefan/7930160/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(N3C(=O)C4=CC=CC=C4C3=O)CC2)=CC=C1F) `REAL300000082829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082829 none O=C([O-])C1=CC(N=NC2CCC(N3C(=O)C4=CC=CC=C4C3=O)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 28, 23, 23, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 23, 23] 36 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 40, 41, 43, 23, 24, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 36, 37, 38, 39, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082829 none O=C([O-])C1=CC(N=NC2CCC(N3C(=O)C4=CC=CC=C4C3=O)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 36, 36, 36, 36, 23, 23, 23, 23, 1, 1] 36 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082829 none O=C([O-])C1=CC(N=NC2CCC(N3C(=O)C4=CC=CC=C4C3=O)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 31, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 36, 36] 36 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082829 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082829 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082829/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082829 Building REAL300000082830 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082830' /scratch/stefan/7930160/working/building/REAL300000082830 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082830 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082830/0 /scratch/stefan/7930160/working/building/REAL300000082830 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/898 `/scratch/stefan/7930160/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC([N+](=O)[O-])=C1) `REAL300000082830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082830 none CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 201, 201, 201, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 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]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082830 none CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 112, 199, 201, 171, 201, 201, 201, 201, 201, 43, 43, 43, 42, 1, 1, 1, 112, 112, 201, 201, 171, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082830 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082830 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082830/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082830 Building REAL300000082831 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082831' /scratch/stefan/7930160/working/building/REAL300000082831 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082831 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082831/0 /scratch/stefan/7930160/working/building/REAL300000082831 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/899 `/scratch/stefan/7930160/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl) `REAL300000082831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082831 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [23, 9, 1, 9, 9, 52, 162, 162, 162, 162, 162, 162, 180, 180, 162, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 52, 162, 162, 162, 1, 1, 1] 186 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 409 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082831 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [103, 48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 162, 162, 80, 162, 162, 162, 162, 103, 103, 103, 103, 103, 11, 1, 1, 1, 162, 162, 162] 186 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 833 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082831 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082831 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082831/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082831 Building REAL300000082832 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082832' /scratch/stefan/7930160/working/building/REAL300000082832 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082832 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082832/0 /scratch/stefan/7930160/working/building/REAL300000082832 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/900 `/scratch/stefan/7930160/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1) `REAL300000082832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082832 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 56, 174, 174, 174, 174, 174, 174, 200, 200, 173, 1, 1, 1, 1, 1, 5, 5, 1, 1, 10, 10, 10, 56, 174, 174, 173, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [1, 40, 14, 15, 16, 17, 18, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 424 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: REAL300000082832 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 173, 174, 173, 174, 201, 201, 173, 173, 60, 60, 60, 12, 1, 1, 1, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 173] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 413 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082832 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082832 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082832/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082832 Building REAL300000082833 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082833' /scratch/stefan/7930160/working/building/REAL300000082833 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082833 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082833/0 /scratch/stefan/7930160/working/building/REAL300000082833 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/901 `/scratch/stefan/7930160/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CSC(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1) `REAL300000082833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082833 none CN1C=C(C2=CSC(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 62, 63, 118, 118, 118, 118, 118, 118, 140, 140, 118, 1, 8, 8, 9, 9, 9, 8, 1, 8, 8, 118, 118, 118, 9] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) 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: REAL300000082833 none CN1C=C(C2=CSC(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 9, 45, 161, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 2, 2, 2, 1, 9, 44, 45, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082833 none CN1C=C(C2=CSC(CN=NC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 117, 117, 117, 26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 117, 200, 201, 201, 201, 201, 201, 117, 26, 26, 1, 1, 1, 200] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082833 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082833/1 /scratch/stefan/7930160/working/building/REAL300000082833 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/902 `/scratch/stefan/7930160/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CSC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1) `REAL300000082833.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082833 none CN1C=C(C2=CSC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 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, 4, 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: [12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 37, 77, 77, 77, 77, 77, 77, 115, 115, 77, 1, 12, 12, 13, 13, 13, 12, 1, 7, 37, 77, 77, 77, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082833 none CN1C=C(C2=CSC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 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, 4, 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, 12, 12, 12, 12, 58, 58, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 12, 58, 156, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082833 none CN1C=C(C2=CSC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 1, 8, 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, 4, 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, 77, 77, 77, 77, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 201, 201, 201, 201, 201, 201, 77, 32, 8, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082833 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082833 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082833/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082833/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082833 Building REAL300000082834 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082834' /scratch/stefan/7930160/working/building/REAL300000082834 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082834 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082834/0 /scratch/stefan/7930160/working/building/REAL300000082834 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/903 `/scratch/stefan/7930160/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=CC=C1F) `REAL300000082834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082834 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 69, 51, 51, 30, 6, 6, 1, 1, 1, 1, 1, 9, 19, 19, 9, 19, 19, 19, 1, 1, 51, 51, 51, 51, 51, 29, 6, 1, 9, 9, 19, 19, 19, 19, 1, 51, 51] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082834 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 25, 51, 51, 51, 154, 201, 201, 154, 201, 201, 201, 51, 51, 1, 1, 1, 1, 1, 7, 25, 51, 154, 154, 201, 201, 201, 201, 51, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24, 25, 26, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082834 none O=C([O-])C1=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 143, 58, 58, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 201, 143, 58, 19, 4, 4, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 462 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082834 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082834 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082834/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082834 Building REAL300000082835 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082835' /scratch/stefan/7930160/working/building/REAL300000082835 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082835 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082835/0 /scratch/stefan/7930160/working/building/REAL300000082835 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/904 `/scratch/stefan/7930160/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082835 none CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 4, 7, 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, 190, 201, 82, 82, 82, 55, 82, 82, 82, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 28, 8, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082835 none CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 4, 7, 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: [24, 9, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 82, 82, 82, 82, 82, 82, 100, 100, 82, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 7, 33, 82, 82, 82] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082835 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082835 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082835/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082835 Building REAL300000082836 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082836' /scratch/stefan/7930160/working/building/REAL300000082836 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082836 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082836/0 /scratch/stefan/7930160/working/building/REAL300000082836 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/905 `/scratch/stefan/7930160/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1) `REAL300000082836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082836 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 53, 133, 133, 133, 133, 133, 133, 134, 134, 133, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 53, 133, 133, 133, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 134 rigid atoms, others: [1, 43, 14, 15, 16, 17, 18, 22, 23] set([0, 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, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082836 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 133, 133, 133, 133, 134, 134, 134, 133, 133, 49, 49, 49, 10, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 133] 134 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 214 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082836 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082836 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082836/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082836 Building REAL300000082837 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082837' /scratch/stefan/7930160/working/building/REAL300000082837 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082837 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082837/0 /scratch/stefan/7930160/working/building/REAL300000082837 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/906 `/scratch/stefan/7930160/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC3(CCCCC3)CC2)=CC=C1F) `REAL300000082837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082837 none O=C([O-])C1=CC(N=NC2CCC3(CCCCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 43, 44, 19, 20, 21, 22, 23]) 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: REAL300000082837 none O=C([O-])C1=CC(N=NC2CCC3(CCCCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082837 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082837 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082837/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082837 Building REAL300000082838 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082838' /scratch/stefan/7930160/working/building/REAL300000082838 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082838 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082838/0 /scratch/stefan/7930160/working/building/REAL300000082838 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/907 `/scratch/stefan/7930160/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](C)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082838 none CC(C)[C@H]1CC[C@@H](C)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 31, 49, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 49, 49, 49, 49, 49, 49, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1] 49 rigid atoms, others: [41, 42, 43, 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, 38, 39, 40]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082838 none CC(C)[C@H]1CC[C@@H](C)CC1N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 39, 39, 31, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31] 49 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 35, 36, 33, 38, 37, 39, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082838 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082838 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082838/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082838 Building REAL300000082839 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082839' /scratch/stefan/7930160/working/building/REAL300000082839 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082839 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082839/0 /scratch/stefan/7930160/working/building/REAL300000082839 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/908 `/scratch/stefan/7930160/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082839 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 42, 102, 102, 101, 101, 102, 102, 121, 121, 102, 19, 19, 19, 19, 8, 8, 1, 1, 1, 10, 42, 102, 102, 102] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082839 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 4, 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, 6, 19, 19, 19, 19, 19, 69, 69, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 6, 19, 19, 19, 69, 126, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 38, 39, 40]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082839 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 4, 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, 164, 102, 102, 102, 102, 102, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 164, 164, 102, 102, 102, 33, 9, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 511 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082839 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082839 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082839/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082839 Building REAL300000082840 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082840' /scratch/stefan/7930160/working/building/REAL300000082840 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082840 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082840/0 /scratch/stefan/7930160/working/building/REAL300000082840 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/909 `/scratch/stefan/7930160/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1) `REAL300000082840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082840 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 57, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 105, 105, 105, 1, 1, 1, 1, 1] 105 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082840 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 105, 105, 105, 105, 105, 105, 105, 105, 47, 47, 47, 11, 1, 1, 1, 105, 105, 105, 105, 105] 105 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082840 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082840 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082840/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082840 Building REAL300000082841 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082841' /scratch/stefan/7930160/working/building/REAL300000082841 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082841 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082841/0 /scratch/stefan/7930160/working/building/REAL300000082841 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/910 `/scratch/stefan/7930160/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1) `REAL300000082841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082841 none COCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 7, 1, 7, 38, 38, 108, 108, 108, 108, 108, 108, 151, 151, 108, 1, 1, 1, 1, 1, 1, 53, 53, 53, 24, 24, 7, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 36, 37, 35, 39, 16, 17, 18, 19, 20, 21, 38, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 437 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082841 none COCC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 132, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 108, 108, 108, 108, 108, 182, 182, 182, 132, 132, 47, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 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: 775 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082841 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082841 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082841/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082841 Building REAL300000082842 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082842' /scratch/stefan/7930160/working/building/REAL300000082842 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082842 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082842/0 /scratch/stefan/7930160/working/building/REAL300000082842 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/911 `/scratch/stefan/7930160/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC3(CCCO3)CC2)=CC=C1F) `REAL300000082842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082842 none O=C([O-])C1=CC(N=NC2CCC3(CCCO3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082842 none O=C([O-])C1=CC(N=NC2CCC3(CCCO3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082842 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082842 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082842/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082842 Building REAL300000082843 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082843' /scratch/stefan/7930160/working/building/REAL300000082843 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082843 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082843/0 /scratch/stefan/7930160/working/building/REAL300000082843 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/912 `/scratch/stefan/7930160/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082843 none CCCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 157, 90, 90, 40, 90, 90, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 90, 201, 201, 201, 201, 201, 157, 157, 64, 90, 90, 40, 9, 1, 1, 1, 90] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 887 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082843 none CCCC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [11, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 47, 90, 90, 90, 90, 90, 90, 102, 102, 89, 1, 12, 12, 12, 11, 11, 7, 7, 1, 1, 1, 7, 47, 90, 90, 90, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 37, 21, 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]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082843 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082843 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082843/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082843 Building REAL300000082844 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082844' /scratch/stefan/7930160/working/building/REAL300000082844 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082844 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082844/0 /scratch/stefan/7930160/working/building/REAL300000082844 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/913 `/scratch/stefan/7930160/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC(C(F)(F)F)C2)=CC=C1F) `REAL300000082844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082844 none O=C([O-])C1=CC(N=NC2CCCC(C(F)(F)F)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 26 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 20, 21, 22]) 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: REAL300000082844 none O=C([O-])C1=CC(N=NC2CCCC(C(F)(F)F)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 26 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082844 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082844 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082844/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082844 Building REAL300000082845 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082845' /scratch/stefan/7930160/working/building/REAL300000082845 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082845 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082845/0 /scratch/stefan/7930160/working/building/REAL300000082845 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/914 `/scratch/stefan/7930160/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1) `REAL300000082845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082845 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 77, 156, 156, 156, 156, 156, 156, 171, 171, 156, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 27, 27, 77, 156, 156, 156, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 450 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082845 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 156, 156, 156, 156, 156, 156, 57, 57, 57, 57, 57, 7, 1, 1, 1, 156, 156, 156, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 339 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082845 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082845 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082845/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082845 Building REAL300000082846 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082846' /scratch/stefan/7930160/working/building/REAL300000082846 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082846 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082846/0 /scratch/stefan/7930160/working/building/REAL300000082846 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/915 `/scratch/stefan/7930160/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082846 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 151, 106, 151, 151, 106, 106, 106, 82, 106, 106, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 187, 187, 187, 187, 187, 106, 106, 106, 34, 9, 1, 1, 1] 187 rigid atoms, others: [35, 36, 37, 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]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082846 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 106, 106, 106, 106, 106, 106, 138, 138, 106, 24, 24, 24, 24, 24, 1, 1, 1, 7, 37, 106, 106, 106] 187 rigid atoms, others: [32, 2, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082846 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082846 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082846/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082846 Building REAL300000082847 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082847' /scratch/stefan/7930160/working/building/REAL300000082847 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082847 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082847/0 /scratch/stefan/7930160/working/building/REAL300000082847 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/916 `/scratch/stefan/7930160/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082847 none COC1=C(Br)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 56, 56, 56, 56, 56, 56, 56, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 62, 56, 56, 56, 38, 10, 1, 1, 1] 62 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000082847 none COC1=C(Br)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 23, 56, 56, 56, 56, 56, 56, 62, 62, 56, 3, 3, 3, 1, 1, 1, 5, 23, 56, 56, 56] 62 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082847 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082847 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082847/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082847 Building REAL300000082848 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082848' /scratch/stefan/7930160/working/building/REAL300000082848 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082848 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082848/0 /scratch/stefan/7930160/working/building/REAL300000082848 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/917 `/scratch/stefan/7930160/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2F)=CC=C1F) `REAL300000082848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082848 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 56, 56, 57, 30, 6, 1, 1, 1, 57, 57] 57 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) 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: REAL300000082848 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 44, 44, 57, 57, 49, 57, 57, 57, 57, 1, 1, 1, 1, 1, 11, 44, 57, 57, 57, 1, 1] 57 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082848 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082848 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082848/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082848 Building REAL300000082849 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082849' /scratch/stefan/7930160/working/building/REAL300000082849 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082849 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082849/0 /scratch/stefan/7930160/working/building/REAL300000082849 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/918 `/scratch/stefan/7930160/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(F)=CC(Cl)=C2)=CC=C1F) `REAL300000082849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082849 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 62, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 113, 113, 112, 112, 113, 62, 10, 1, 1, 1, 113, 113] 113 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082849 none O=C([O-])C1=CC(NN=CC2=CC(F)=CC(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 39, 39, 113, 113, 113, 84, 113, 113, 113, 1, 1, 1, 1, 1, 11, 39, 113, 113, 113, 1, 1] 113 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: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082849 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082849 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082849/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082849 Building REAL300000082850 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082850' /scratch/stefan/7930160/working/building/REAL300000082850 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082850 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082850/0 /scratch/stefan/7930160/working/building/REAL300000082850 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/919 `/scratch/stefan/7930160/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21) `REAL300000082850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082850 none CN1C(=O)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 130, 130, 130, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 130, 130, 114, 130, 130, 130, 130, 130, 130, 130, 130, 52, 12, 1, 1, 1, 130, 130] 130 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) 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: REAL300000082850 none CN1C(=O)CCC2=CC(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 52, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 11, 52, 130, 130, 130, 1, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 32, 22, 23, 24, 38, 28, 29, 30, 31] set([33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082850 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082850 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082850/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082850 Building REAL300000082851 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082851' /scratch/stefan/7930160/working/building/REAL300000082851 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082851 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082851/0 /scratch/stefan/7930160/working/building/REAL300000082851 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/920 `/scratch/stefan/7930160/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082851 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 47, 131, 131, 131, 131, 131, 131, 163, 163, 131, 7, 7, 7, 3, 3, 1, 1, 1, 1, 3, 10, 47, 131, 131, 131] 163 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082851 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 7, 7, 30, 86, 86, 86, 86, 86, 86, 127, 127, 86, 3, 3, 3, 1, 1, 3, 3, 3, 3, 1, 7, 30, 86, 86, 86] 163 rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 36, 30, 31] set([0, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082851 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [122, 86, 86, 86, 86, 86, 86, 131, 131, 131, 131, 131, 86, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 122, 122, 122, 86, 86, 131, 131, 131, 131, 86, 46, 10, 1, 1, 1] 163 rigid atoms, others: [39, 40, 41, 16, 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, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082851 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082851 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082851/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082851 Building REAL300000082852 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082852' /scratch/stefan/7930160/working/building/REAL300000082852 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082852 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082852/0 /scratch/stefan/7930160/working/building/REAL300000082852 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/921 `/scratch/stefan/7930160/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1) `REAL300000082852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082852 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 310 conformations in input total number of sets (complete confs): 310 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 60, 155, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 60, 155, 155, 155, 1, 1, 2, 1] 310 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 280 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: REAL300000082852 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 310 conformations in input total number of sets (complete confs): 310 using faster count positions algorithm for large data unique positions, atoms: [53, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 155, 155, 152, 155, 155, 155, 155, 54, 54, 54, 11, 1, 1, 1, 155, 155, 310, 155] 310 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 553 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082852 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082852/1 /scratch/stefan/7930160/working/building/REAL300000082852 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/922 `/scratch/stefan/7930160/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1) `REAL300000082852.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082852 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 48, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 48, 76, 76, 76, 1, 1, 1] 76 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 166 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: REAL300000082852 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 76, 76, 76, 76, 76, 76, 76, 24, 24, 24, 6, 1, 1, 1, 76, 76, 76] 76 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 122 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082852 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082852 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082852/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082852/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082852 Building REAL300000082853 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082853' /scratch/stefan/7930160/working/building/REAL300000082853 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082853 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082853/0 /scratch/stefan/7930160/working/building/REAL300000082853 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/923 `/scratch/stefan/7930160/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1) `REAL300000082853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082853 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 34, 99, 99, 98, 98, 99, 99, 145, 145, 99, 1, 1, 1, 1, 1, 12, 12, 1, 8, 8, 8, 34, 99, 99, 99, 1, 12, 12, 12, 12, 13, 13, 13] 160 rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 402 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082853 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 99, 99, 99, 99, 160, 160, 99, 47, 47, 47, 11, 1, 1, 1, 99, 160, 160, 160, 160, 160, 160, 160] 160 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 492 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082853 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082853/1 /scratch/stefan/7930160/working/building/REAL300000082853 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/924 `/scratch/stefan/7930160/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CS1) `REAL300000082853.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082853 none CC(C)C1=NC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 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, 137, 201, 137, 137, 35, 7, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 137, 137, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 35, 1, 1, 1, 137] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082853 none CC(C)C1=NC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 7, 7, 7, 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: [10, 1, 10, 1, 1, 1, 1, 11, 11, 53, 53, 137, 137, 137, 137, 137, 137, 181, 181, 137, 1, 1, 11, 11, 11, 10, 10, 10, 10, 11, 11, 11, 11, 137, 137, 137, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082853 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082853 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082853/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082853/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082853 Building REAL300000082854 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082854' /scratch/stefan/7930160/working/building/REAL300000082854 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082854 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082854/0 /scratch/stefan/7930160/working/building/REAL300000082854 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/925 `/scratch/stefan/7930160/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1) `REAL300000082854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082854 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 60, 60, 60, 60, 60, 60, 61, 61, 60, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 60, 60, 60, 1, 1, 1] 61 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082854 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 60, 60, 60, 60, 60, 60, 39, 39, 39, 12, 1, 1, 1, 60, 60, 60] 61 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082854 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082854/1 /scratch/stefan/7930160/working/building/REAL300000082854 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/926 `/scratch/stefan/7930160/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1) `REAL300000082854.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082854 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [12, 1, 12, 77, 77, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 150, 150, 150, 1, 1, 1] 150 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082854 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [56, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 150, 150, 150, 150, 150, 150, 56, 56, 56, 56, 1, 1, 1, 150, 150, 150] 150 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082854 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082854 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082854/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082854/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082854 Building REAL300000082855 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082855' /scratch/stefan/7930160/working/building/REAL300000082855 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082855 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082855/0 /scratch/stefan/7930160/working/building/REAL300000082855 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/927 `/scratch/stefan/7930160/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1O) `REAL300000082855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082855 none O=C([O-])C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [49, 32, 49, 32, 32, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 32, 32, 32, 23, 8, 1, 1, 1, 32, 32, 64] 98 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) 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: REAL300000082855 none O=C([O-])C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 16, 32, 32, 31, 31, 32, 32, 49, 49, 32, 1, 1, 1, 1, 1, 5, 16, 32, 32, 32, 1, 1, 2] 98 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 31]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082855 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082855 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082855/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082855 Building REAL300000082856 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082856' /scratch/stefan/7930160/working/building/REAL300000082856 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082856 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082856/0 /scratch/stefan/7930160/working/building/REAL300000082856 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/928 `/scratch/stefan/7930160/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCNC3=CC=CC=C32)=CC=C1F) `REAL300000082856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082856 none O=C([O-])C1=CC(NN=C2CCCNC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 34, 35, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 36, 37]) 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: REAL300000082856 none O=C([O-])C1=CC(NN=C2CCCNC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082856 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082856 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082856/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082856 Building REAL300000082857 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082857' /scratch/stefan/7930160/working/building/REAL300000082857 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082857 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082857/0 /scratch/stefan/7930160/working/building/REAL300000082857 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/929 `/scratch/stefan/7930160/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1) `REAL300000082857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082857 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 28, 84, 84, 84, 84, 84, 84, 90, 90, 84, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 6, 6, 6, 28, 84, 84, 84, 1, 1, 11, 11, 11, 11, 11, 11, 32, 1, 1] 366 rigid atoms, others: [32, 1, 40, 41, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 240 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: REAL300000082857 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 84, 84, 48, 80, 122, 122, 122, 84, 84, 40, 40, 40, 9, 1, 1, 1, 84, 84, 122, 122, 122, 122, 122, 122, 366, 84, 84] 366 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 870 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082857 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082857 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082857/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082857 Building REAL300000082858 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082858' /scratch/stefan/7930160/working/building/REAL300000082858 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082858 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082858/0 /scratch/stefan/7930160/working/building/REAL300000082858 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/930 `/scratch/stefan/7930160/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O) `REAL300000082858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082858 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 53, 126, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 126, 126, 126, 1, 1, 2, 2, 2, 2] 252 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 239 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082858 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 126, 126, 126, 79, 126, 126, 126, 126, 45, 45, 45, 11, 1, 1, 1, 126, 126, 126, 126, 126, 252] 252 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 641 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082858 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082858 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082858/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082858 Building REAL300000082859 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082859' /scratch/stefan/7930160/working/building/REAL300000082859 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082859 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082859/0 /scratch/stefan/7930160/working/building/REAL300000082859 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/931 `/scratch/stefan/7930160/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F) `REAL300000082859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082859 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 71, 71, 168, 168, 168, 168, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 168, 168, 168, 1, 1] 168 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082859 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [56, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 168, 168, 168, 168, 168, 168, 168, 56, 56, 56, 56, 1, 1, 1, 168, 168] 168 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082859 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082859/1 /scratch/stefan/7930160/working/building/REAL300000082859 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/932 `/scratch/stefan/7930160/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F) `REAL300000082859.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082859 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 65, 113, 113, 112, 112, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 113, 113, 113, 1, 1] 113 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 244 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082859 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 113, 113, 113, 113, 113, 113, 113, 39, 39, 39, 11, 1, 1, 1, 113, 113] 113 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082859 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082859 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082859/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082859/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082859 Building REAL300000082860 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082860' /scratch/stefan/7930160/working/building/REAL300000082860 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082860 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082860/0 /scratch/stefan/7930160/working/building/REAL300000082860 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/933 `/scratch/stefan/7930160/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C=C1C)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCS2) `REAL300000082860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082860 none CC1=CC2=C(C=C1C)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCS2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 40, 40, 40, 40] 40 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 67 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: REAL300000082860 none CC1=CC2=C(C=C1C)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CCS2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 8, 40, 40, 40, 1, 1, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 38, 21, 22, 23, 36, 27, 28, 37] set([32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082860 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082860 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082860/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082860 Building REAL300000082861 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082861' /scratch/stefan/7930160/working/building/REAL300000082861 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082861 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082861/0 /scratch/stefan/7930160/working/building/REAL300000082861 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/934 `/scratch/stefan/7930160/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1) `REAL300000082861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082861 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 59, 59, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 200 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: REAL300000082861 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 69, 131, 131, 131, 131, 131, 131, 131, 69, 69, 69, 69, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 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: 416 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082861 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082861 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082861/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082861 Building REAL300000082862 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082862' /scratch/stefan/7930160/working/building/REAL300000082862 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082862 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082862/0 /scratch/stefan/7930160/working/building/REAL300000082862 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/935 `/scratch/stefan/7930160/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082862 none C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 141, 82, 82, 82, 39, 82, 82, 82, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 82, 82, 82, 20, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082862 none C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 82, 82, 82, 82, 82, 82, 112, 112, 82, 40, 40, 40, 1, 1, 1, 10, 36, 82, 82, 82] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082862 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082862 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082862/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082862 Building REAL300000082863 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082863' /scratch/stefan/7930160/working/building/REAL300000082863 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082863 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082863/0 /scratch/stefan/7930160/working/building/REAL300000082863 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/936 `/scratch/stefan/7930160/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1) `REAL300000082863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082863 none COC1=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 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, 180, 180, 41, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 180, 180, 180, 201, 201, 201, 42, 42, 42, 10, 1, 1, 1, 180, 180] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 284 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082863 none COC1=C(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 12, 12, 12, 77, 180, 180, 180, 180, 180, 180, 199, 199, 180, 1, 1, 1, 3, 3, 3, 13, 13, 13, 77, 180, 180, 180, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 18, 19, 20, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 417 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082863 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082863/1 /scratch/stefan/7930160/working/building/REAL300000082863 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/937 `/scratch/stefan/7930160/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1) `REAL300000082863.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082863 none COC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 173, 173, 58, 8, 58, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 173, 173, 173, 201, 201, 201, 58, 58, 58, 58, 1, 1, 1, 173, 173] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000082863 none COC1=C(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 64, 64, 173, 173, 173, 173, 173, 173, 190, 190, 173, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 173, 173, 173, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 18, 19, 20, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 327 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082863 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082863 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082863/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082863/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082863 Building REAL300000082864 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082864' /scratch/stefan/7930160/working/building/REAL300000082864 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082864 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082864/0 /scratch/stefan/7930160/working/building/REAL300000082864 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/938 `/scratch/stefan/7930160/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCCCC2=CC=C3OCCC3=C2)=CC=C1F) `REAL300000082864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082864 none O=C([O-])C1=CC(N=NCCCC2=CC=C3OCCC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 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, 112, 112, 25, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 25, 25, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39]) 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: REAL300000082864 none O=C([O-])C1=CC(N=NCCCC2=CC=C3OCCC3=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 9, 9, 41, 58, 111, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 40, 41, 78, 78, 101, 102, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082864 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082864 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082864/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082864 Building REAL300000082865 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082865' /scratch/stefan/7930160/working/building/REAL300000082865 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082865 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082865/0 /scratch/stefan/7930160/working/building/REAL300000082865 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/939 `/scratch/stefan/7930160/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1) `REAL300000082865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082865 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 25, 25, 68, 68, 68, 68, 68, 68, 78, 78, 68, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 68, 68, 68, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082865 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 68, 78, 78, 76, 78, 78, 68, 68, 68, 68, 26, 26, 26, 26, 1, 1, 1, 78, 78, 76, 78, 78, 68, 68, 68, 68, 68, 68, 68, 68] 78 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082865 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 31, 31, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 78, 78, 78, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 78 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082865 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082865 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082865/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082865 Building REAL300000082866 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082866' /scratch/stefan/7930160/working/building/REAL300000082866 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082866 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082866/0 /scratch/stefan/7930160/working/building/REAL300000082866 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/940 `/scratch/stefan/7930160/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082866 none CCOC(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 153, 34, 153, 34, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 201, 201, 201, 201, 201, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 34, 34] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082866 none CCOC(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 24, 13, 1, 13, 1, 1, 1, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 34, 51, 51, 34, 1, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 39, 40, 35, 22, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 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/7930160/working/building/REAL300000082866 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082866 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082866/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082866 Building REAL300000082867 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082867' /scratch/stefan/7930160/working/building/REAL300000082867 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082867 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082867/0 /scratch/stefan/7930160/working/building/REAL300000082867 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/941 `/scratch/stefan/7930160/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082867 none CCN1N=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 68, 68, 68, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 68, 68, 68, 68, 113, 113, 113, 113, 113, 41, 11, 1, 1, 1, 68, 68, 67, 68] 113 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082867 none CCN1N=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [5, 1, 1, 1, 1, 1, 7, 7, 26, 68, 68, 68, 68, 68, 68, 101, 101, 68, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 26, 68, 68, 68, 1, 1, 1, 1] 113 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 22, 23, 36, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082867 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082867/1 /scratch/stefan/7930160/working/building/REAL300000082867 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/942 `/scratch/stefan/7930160/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082867.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082867 none CCN1N=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 92, 92, 92, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 92, 92, 92, 201, 201, 201, 201, 201, 30, 31, 1, 1, 1, 92, 92, 92, 92] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082867 none CCN1N=C(CN=NC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 8, 48, 48, 92, 92, 92, 92, 92, 92, 135, 135, 92, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5, 7, 7, 92, 92, 92, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 22, 23, 36, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082867 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082867 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082867/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082867/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082867 Building REAL300000082868 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082868' /scratch/stefan/7930160/working/building/REAL300000082868 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082868 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082868/0 /scratch/stefan/7930160/working/building/REAL300000082868 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/943 `/scratch/stefan/7930160/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082868 none CCSC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 189, 108, 108, 108, 108, 108, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 201, 201, 201, 201, 201, 108, 108, 108, 41, 11, 1, 1, 1, 108] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 354 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: REAL300000082868 none CCSC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 108, 108, 108, 108, 108, 108, 122, 122, 108, 1, 27, 27, 27, 27, 27, 1, 1, 1, 10, 49, 108, 108, 108, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 35, 21, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 344 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082868 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082868 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082868/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082868 Building REAL300000082869 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082869' /scratch/stefan/7930160/working/building/REAL300000082869 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082869 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082869/0 /scratch/stefan/7930160/working/building/REAL300000082869 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/944 `/scratch/stefan/7930160/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F) `REAL300000082869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082869 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 58, 57, 57, 201, 201, 157, 201, 201, 201, 58, 58, 58, 57, 24, 8, 1, 1, 1, 58, 58, 58, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082869 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 33, 58, 58, 58, 58, 58, 58, 69, 69, 57, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 2, 2, 2, 1, 7, 33, 58, 58, 57, 2, 2, 2, 7, 7, 6, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082869 none CC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 38, 105, 201, 201, 201, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 394 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082869 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082869 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082869/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082869 Building REAL300000082870 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082870' /scratch/stefan/7930160/working/building/REAL300000082870 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082870 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082870/0 /scratch/stefan/7930160/working/building/REAL300000082870 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/945 `/scratch/stefan/7930160/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082870 none CC1=CC=C(C)C2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 1, 1, 1] 44 rigid atoms, others: [39, 40, 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, 38]) total number of confs: 71 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: REAL300000082870 none CC1=CC=C(C)C2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 44, 44, 44] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 32, 33, 34, 35, 36, 37] set([38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082870 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082870 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082870/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082870 Building REAL300000082871 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082871' /scratch/stefan/7930160/working/building/REAL300000082871 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082871 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082871/0 /scratch/stefan/7930160/working/building/REAL300000082871 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/946 `/scratch/stefan/7930160/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082871 none COC1=CC=CC2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 93, 93, 93, 55, 55, 55, 55, 55, 55, 55, 55, 55, 10, 1, 1, 1] 93 rigid atoms, others: [37, 38, 39, 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]) 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: REAL300000082871 none COC1=CC=CC2=C1CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 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, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 55, 55, 55, 55, 93, 93, 55, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 55] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 234 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082871 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082871 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082871/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082871 Building REAL300000082872 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082872' /scratch/stefan/7930160/working/building/REAL300000082872 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082872 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082872/0 /scratch/stefan/7930160/working/building/REAL300000082872 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/947 `/scratch/stefan/7930160/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC=C(Br)C=C32)=CC=C1F) `REAL300000082872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082872 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31] 31 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 43 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: REAL300000082872 none O=C([O-])C1=CC(NN=C2CCC3=CC=C(Br)C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082872 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082872 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082872/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082872 Building REAL300000082873 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082873' /scratch/stefan/7930160/working/building/REAL300000082873 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082873 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082873/0 /scratch/stefan/7930160/working/building/REAL300000082873 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/948 `/scratch/stefan/7930160/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300000082873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082873 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 37, 12, 1, 12, 12, 67, 178, 178, 177, 177, 178, 178, 194, 194, 178, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 34, 34, 67, 178, 178, 178, 1, 1, 1, 1] 201 rigid atoms, others: [4, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 501 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082873 none CC(C)CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 74, 76, 42, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 178, 178, 119, 178, 178, 178, 76, 76, 76, 76, 76, 76, 76, 74, 74, 10, 1, 1, 1, 178, 178, 147, 178] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 615 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082873 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082873 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082873/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082873 Building REAL300000082874 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082874' /scratch/stefan/7930160/working/building/REAL300000082874 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082874 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082874/0 /scratch/stefan/7930160/working/building/REAL300000082874 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/949 `/scratch/stefan/7930160/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=CC=C1F) `REAL300000082874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082874 none O=C([O-])C1=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 38, 38, 39, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 25, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082874 none O=C([O-])C1=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 38, 1, 1, 1, 1, 1, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082874 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082874 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082874/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082874 Building REAL300000082875 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082875' /scratch/stefan/7930160/working/building/REAL300000082875 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082875 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082875/0 /scratch/stefan/7930160/working/building/REAL300000082875 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/950 `/scratch/stefan/7930160/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082875 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 38, 74, 74, 74, 74, 74, 74, 74, 74, 74, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 16, 38, 74, 74, 74] 74 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082875 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 11, 38, 74, 74, 74, 74, 74, 74, 74, 74, 74, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 11, 37, 74, 74, 74] 74 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082875 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 3, 7, 7, 7, 7, 7, 4, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 30, 9, 1, 1, 1] 74 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082875 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082875 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082875/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082875 Building REAL300000082876 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082876' /scratch/stefan/7930160/working/building/REAL300000082876 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082876 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082876/0 /scratch/stefan/7930160/working/building/REAL300000082876 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/951 `/scratch/stefan/7930160/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1) `REAL300000082876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082876 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [88, 88, 88, 88, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 88, 88, 144, 144, 144, 144, 144, 88, 88, 88, 88, 88, 88, 38, 9, 1, 1, 1, 144, 144, 144, 144, 144, 88] 144 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082876 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 39, 88, 88, 88, 88, 88, 88, 113, 113, 88, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 1, 10, 39, 88, 88, 88, 7, 7, 7, 7, 7, 1] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 18, 19, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082876 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 6, 7, 7, 7, 26, 26, 87, 144, 144, 144, 144, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 87, 144, 144, 144, 1, 1, 2, 2, 2, 7] 144 rigid atoms, others: [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, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 309 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082876 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082876 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082876/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082876 Building REAL300000082877 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082877' /scratch/stefan/7930160/working/building/REAL300000082877 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082877 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082877/0 /scratch/stefan/7930160/working/building/REAL300000082877 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/952 `/scratch/stefan/7930160/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=CC=C1F) `REAL300000082877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082877 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 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: [56, 37, 56, 37, 37, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 6, 6, 6, 1, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 37, 37] 86 rigid atoms, others: [32, 33, 38, 7, 8, 9, 10, 11, 12, 22, 39, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 34, 35, 36, 37, 40, 41]) total number of confs: 156 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: REAL300000082877 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 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: [3, 1, 3, 1, 1, 1, 1, 9, 9, 37, 37, 37, 37, 86, 86, 47, 66, 86, 86, 86, 86, 86, 37, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 86, 86, 86, 86, 35, 37, 1, 1] 86 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 403 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082877 none O=C([O-])C1=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7, 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, 34, 34, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 86, 86, 86, 86, 86, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 86, 86] 86 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082877 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082877 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082877/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082877 Building REAL300000082878 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082878' /scratch/stefan/7930160/working/building/REAL300000082878 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082878 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082878/0 /scratch/stefan/7930160/working/building/REAL300000082878 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/953 `/scratch/stefan/7930160/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1) `REAL300000082878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082878 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [11, 1, 11, 11, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 64, 201, 201, 201, 1, 1, 2, 2, 1] 201 rigid atoms, others: [32, 1, 35, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 352 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: REAL300000082878 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 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: [58, 59, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 201, 201, 59, 59, 201, 201, 201, 201, 201, 59, 59, 59, 11, 1, 1, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 912 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082878 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082878 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082878/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082878 Building REAL300000082879 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082879' /scratch/stefan/7930160/working/building/REAL300000082879 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082879 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082879/0 /scratch/stefan/7930160/working/building/REAL300000082879 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/954 `/scratch/stefan/7930160/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C21) `REAL300000082879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082879 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 56, 11, 1, 1, 1, 125, 125, 125] 125 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082879 none CN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(F)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 10, 10, 56, 125, 125, 124, 124, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 56, 125, 125, 125, 1, 1, 1] 125 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 17, 18, 19, 20, 21, 22, 23, 27] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082879 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082879 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082879/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082879 Building REAL300000082880 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082880' /scratch/stefan/7930160/working/building/REAL300000082880 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082880 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082880/0 /scratch/stefan/7930160/working/building/REAL300000082880 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/955 `/scratch/stefan/7930160/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NNC(C(F)(F)F)=C2)=CC=C1F) `REAL300000082880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082880 none O=C([O-])C1=CC(NN=CC2=NNC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 8, 8, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 29, 7, 1, 1, 55, 55] 55 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000082880 none O=C([O-])C1=CC(NN=CC2=NNC(C(F)(F)F)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.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, 8, 8, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 44, 44, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 11, 44, 55, 55, 1, 1] 55 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082880 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082880/1 /scratch/stefan/7930160/working/building/REAL300000082880 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/956 `/scratch/stefan/7930160/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=NN2)=CC=C1F) `REAL300000082880.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082880 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=NN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 33, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 85, 85, 85, 85, 85, 33, 7, 1, 1, 85, 85] 85 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000082880 none O=C([O-])C1=CC(NN=CC2=CC(C(F)(F)F)=NN2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 12, 57, 57, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 12, 57, 85, 85, 1, 1] 85 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082880 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082880 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082880/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082880/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082880 Building REAL300000082881 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082881' /scratch/stefan/7930160/working/building/REAL300000082881 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082881 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082881/0 /scratch/stefan/7930160/working/building/REAL300000082881 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/957 `/scratch/stefan/7930160/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC(Br)=CC=C32)=CC=C1F) `REAL300000082881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082881 none O=C([O-])C1=CC(NN=C2CCCC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 24]) total number of confs: 54 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: REAL300000082881 none O=C([O-])C1=CC(NN=C2CCCC3=CC(Br)=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1] 36 rigid atoms, others: [1, 34, 3, 4, 5, 6, 19, 20, 21, 22, 23, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082881 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082881 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082881/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082881 Building REAL300000082882 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082882' /scratch/stefan/7930160/working/building/REAL300000082882 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082882 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082882/0 /scratch/stefan/7930160/working/building/REAL300000082882 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/958 `/scratch/stefan/7930160/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CN=C3)C2)=CC=C1F) `REAL300000082882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082882 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CN=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [67, 47, 67, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 47, 47] 116 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 13, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 33, 34, 35, 36, 39, 40]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082882 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CN=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 47, 47, 47, 47, 47, 116, 116, 116, 116, 116, 47, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 116, 116, 116, 116, 47, 47, 1, 1] 116 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082882 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CN=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 61, 61, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 116, 116, 116, 116, 116, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 116, 116] 116 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082882 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082882 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082882/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082882 Building REAL300000082883 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082883' /scratch/stefan/7930160/working/building/REAL300000082883 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082883 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082883/0 /scratch/stefan/7930160/working/building/REAL300000082883 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/959 `/scratch/stefan/7930160/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C#N) `REAL300000082883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082883 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 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, 160, 160, 160, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 160, 160, 160, 160, 160, 201, 201, 201, 160, 70, 13, 1, 1, 1, 160, 160] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082883 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 51, 160, 160, 160, 160, 160, 160, 201, 201, 160, 1, 1, 1, 1, 1, 3, 3, 3, 1, 10, 51, 160, 160, 160, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 18, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082883 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082883 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082883/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082883 Building REAL300000082884 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082884' /scratch/stefan/7930160/working/building/REAL300000082884 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082884 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082884/0 /scratch/stefan/7930160/working/building/REAL300000082884 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/960 `/scratch/stefan/7930160/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1) `REAL300000082884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082884 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [110, 110, 110, 110, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 110, 110, 164, 164, 164, 164, 164, 110, 110, 110, 110, 110, 110, 39, 9, 1, 1, 1, 164, 164, 164, 164, 164, 110] 164 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082884 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 49, 110, 110, 110, 110, 110, 110, 131, 131, 110, 1, 1, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 1, 10, 49, 110, 110, 110, 9, 9, 9, 9, 9, 1] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 18, 19, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082884 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [9, 9, 8, 9, 9, 9, 37, 37, 107, 164, 164, 164, 164, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 37, 107, 164, 164, 164, 1, 2, 2, 2, 1, 9] 164 rigid atoms, others: [36, 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, 37, 38, 39, 41]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082884 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082884 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082884/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082884 Building REAL300000082885 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082885' /scratch/stefan/7930160/working/building/REAL300000082885 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082885 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082885/0 /scratch/stefan/7930160/working/building/REAL300000082885 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/961 `/scratch/stefan/7930160/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=CC=C1F) `REAL300000082885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082885 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [124, 115, 124, 115, 115, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 4, 4, 5, 5, 115, 115, 115, 115, 115, 40, 11, 1, 1, 5, 5, 5, 5, 115, 115] 125 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082885 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 44, 44, 115, 115, 115, 115, 115, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 10, 44, 115, 115, 125, 125, 125, 125, 1, 1] 125 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082885 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 48, 14, 14, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 48, 14, 5, 5, 1, 1, 1, 1, 125, 125] 125 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082885 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082885 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082885/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082885 Building REAL300000082886 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082886' /scratch/stefan/7930160/working/building/REAL300000082886 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082886 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082886/0 /scratch/stefan/7930160/working/building/REAL300000082886 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/962 `/scratch/stefan/7930160/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082886 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 51, 109, 109, 109, 109, 109, 109, 141, 141, 109, 9, 9, 9, 9, 9, 9, 9, 1, 1, 13, 51, 109, 109, 109] 199 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 349 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: REAL300000082886 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 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, 1, 9, 9, 9, 9, 9, 39, 39, 130, 199, 199, 199, 199, 199, 199, 199, 199, 199, 2, 2, 2, 1, 1, 1, 1, 9, 9, 39, 130, 199, 199, 199] 199 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([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]) total number of confs: 442 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082886 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 4, 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 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, 109, 109, 109, 109, 109, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 199, 199, 199, 199, 199, 199, 199, 109, 109, 35, 7, 1, 1, 1] 199 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 296 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082886 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082886 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082886/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082886 Building REAL300000082887 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082887' /scratch/stefan/7930160/working/building/REAL300000082887 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082887 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082887/0 /scratch/stefan/7930160/working/building/REAL300000082887 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/963 `/scratch/stefan/7930160/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=N1) `REAL300000082887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082887 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 40, 93, 93, 93, 93, 93, 93, 119, 119, 93, 1, 12, 12, 13, 13, 13, 12, 1, 1, 7, 40, 93, 93, 93, 12] 178 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082887 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 64, 64, 156, 178, 178, 178, 178, 178, 178, 178, 178, 178, 12, 1, 1, 2, 2, 2, 1, 12, 12, 64, 155, 178, 178, 178, 1] 178 rigid atoms, others: [0, 1, 2, 3, 4, 35, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082887 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 93, 93, 93, 93, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 93, 177, 177, 178, 178, 178, 177, 93, 93, 38, 8, 1, 1, 1, 177] 178 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 276 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082887 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082887 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082887/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082887 Building REAL300000082888 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082888' /scratch/stefan/7930160/working/building/REAL300000082888 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082888 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082888/0 /scratch/stefan/7930160/working/building/REAL300000082888 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/964 `/scratch/stefan/7930160/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC=C1C(F)(F)F) `REAL300000082888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082888 none CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 3, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 47, 47, 47, 2, 2, 1, 1, 1, 1] 47 rigid atoms, others: [35, 36, 37, 38, 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]) 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: REAL300000082888 none CC(=CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 30, 1, 1, 1, 47, 47, 47, 47, 47, 47] 47 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082888 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082888 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082888/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082888 Building REAL300000082889 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082889' /scratch/stefan/7930160/working/building/REAL300000082889 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082889 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082889/0 /scratch/stefan/7930160/working/building/REAL300000082889 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/965 `/scratch/stefan/7930160/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1) `REAL300000082889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082889 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 55, 55, 55, 55, 157, 157, 157, 55, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 128, 128, 128, 128, 128, 157, 157, 157, 55, 30, 8, 1, 1, 1] 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]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082889 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 10, 10, 10, 1, 1, 1, 6, 6, 28, 55, 55, 55, 55, 55, 55, 93, 93, 55, 1, 6, 6, 6, 6, 6, 10, 10, 10, 1, 6, 28, 55, 55, 55] 201 rigid atoms, others: [32, 1, 2, 3, 4, 8, 9, 10, 23] set([0, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082889 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082889 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082889/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082889 Building REAL300000082890 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082890' /scratch/stefan/7930160/working/building/REAL300000082890 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082890 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082890/0 /scratch/stefan/7930160/working/building/REAL300000082890 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/966 `/scratch/stefan/7930160/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082890 none CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 133, 134, 134, 80, 44, 80, 44, 44, 44, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 134, 134, 134, 134, 134, 134, 134, 134, 134, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 44, 44, 44, 44] 134 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 46, 24, 47, 21] 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, 40, 41, 42, 43, 44, 48, 49, 50, 51]) total number of confs: 333 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082890 none CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [19, 15, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 44, 44, 44, 44, 44, 44, 64, 64, 44, 1, 1, 20, 20, 20, 19, 19, 19, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 1, 1, 1, 1] 134 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 196 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082890 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082890 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082890/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082890 Building REAL300000082891 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082891' /scratch/stefan/7930160/working/building/REAL300000082891 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082891 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082891/0 /scratch/stefan/7930160/working/building/REAL300000082891 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/967 `/scratch/stefan/7930160/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 12, 18, 18, 12, 18, 18, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 22, 22, 16, 1, 1, 7, 7, 7, 12, 12, 18, 18, 12, 18, 18, 1, 1, 1, 1, 1, 1, 16, 16, 16, 1, 1, 1, 1] 53 rigid atoms, others: [1, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 49, 50, 26, 27, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 48, 48, 53, 53, 53, 53, 53, 53, 53, 53, 53, 18, 18, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 53, 53, 53, 18, 18, 18, 18] 53 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [36, 16, 36, 36, 49, 53, 53, 49, 53, 53, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 16, 16, 36, 36, 36, 49, 49, 53, 53, 49, 53, 53, 16, 16, 16, 16, 16, 16, 1, 1, 1, 16, 16, 16, 16] 53 rigid atoms, others: [44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082891 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082891/1 /scratch/stefan/7930160/working/building/REAL300000082891 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/968 `/scratch/stefan/7930160/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082891.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 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: [6, 1, 6, 6, 13, 21, 21, 20, 21, 21, 1, 1, 1, 1, 1, 13, 13, 51, 51, 51, 51, 51, 51, 73, 73, 51, 1, 1, 7, 7, 7, 13, 13, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 51, 51, 51, 1, 1, 1, 1] 150 rigid atoms, others: [1, 43, 38, 39, 40, 41, 10, 11, 12, 13, 14, 47, 48, 49, 50, 26, 27, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 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: [8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 100, 100, 150, 150, 150, 150, 150, 150, 150, 150, 150, 21, 21, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 150, 150, 150, 21, 21, 21, 21] 150 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 249 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082891 none C[N@@H+](CC1=CC=CC=C1)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 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, 7, 7, 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: [122, 51, 122, 122, 147, 150, 150, 148, 150, 150, 51, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 51, 122, 122, 122, 147, 147, 150, 150, 150, 150, 150, 51, 51, 51, 51, 51, 51, 1, 1, 1, 51, 51, 51, 51] 150 rigid atoms, others: [44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 583 number of broken/clashed sets: 126 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082891 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082891 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082891/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082891/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082891 Building REAL300000082892 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082892' /scratch/stefan/7930160/working/building/REAL300000082892 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082892 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082892/0 /scratch/stefan/7930160/working/building/REAL300000082892 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/969 `/scratch/stefan/7930160/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082892 none COCCCN1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 177, 115, 97, 47, 47, 47, 47, 47, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 177, 177, 115, 115, 97, 97, 47, 47, 18, 6, 1, 1, 1] 201 rigid atoms, others: [36, 37, 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, 35]) 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: REAL300000082892 none COCCCN1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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: [53, 21, 9, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 47, 47, 47, 47, 47, 47, 72, 72, 47, 54, 54, 54, 21, 21, 9, 9, 5, 5, 1, 1, 6, 18, 47, 47, 47] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082892 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082892 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082892/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082892 Building REAL300000082893 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082893' /scratch/stefan/7930160/working/building/REAL300000082893 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082893 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082893/0 /scratch/stefan/7930160/working/building/REAL300000082893 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/970 `/scratch/stefan/7930160/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(C(F)F)CC2)=CC=C1F) `REAL300000082893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082893 none O=C([O-])C1=CC(N=NC2CCC(C(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 64, 46, 46, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 46, 46] 64 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 13, 14, 34, 17, 18, 19, 20, 21, 28]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082893 none O=C([O-])C1=CC(N=NC2CCC(C(F)F)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 64, 64, 46, 46, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 64, 46, 46, 46, 46, 1, 1] 64 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082893 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082893 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082893/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082893 Building REAL300000082894 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082894' /scratch/stefan/7930160/working/building/REAL300000082894 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082894 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082894/0 /scratch/stefan/7930160/working/building/REAL300000082894 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/971 `/scratch/stefan/7930160/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082894 none CC1=CC=CN=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 45, 45, 26, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 1, 1] 60 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 24, 38, 42, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 39, 40, 41]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082894 none CC1=CC=CN=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 1, 4, 4, 4, 4, 4, 19, 19, 60, 60, 60, 60, 60, 60, 60, 60, 60, 4, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 60, 60, 60, 4, 4] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082894 none CC1=CC=CN=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 60, 60, 60, 60, 60, 60, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26] 60 rigid atoms, others: [39, 40, 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, 38, 42, 43]) total number of confs: 114 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082894 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082894 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082894/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082894 Building REAL300000082895 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082895' /scratch/stefan/7930160/working/building/REAL300000082895 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082895 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082895/0 /scratch/stefan/7930160/working/building/REAL300000082895 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/972 `/scratch/stefan/7930160/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1F) `REAL300000082895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082895 none COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 108, 108, 108, 108, 108, 60, 60, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 123, 123, 123, 108, 108, 108, 60, 10, 1, 1, 1] 123 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]) 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: REAL300000082895 none COC1=CC=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 108, 108, 108, 108, 108, 108, 123, 123, 108, 1, 1, 4, 4, 4, 1, 1, 1, 9, 35, 108, 108, 108] 123 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 25, 26, 27] set([0, 32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082895 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082895 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082895/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082895 Building REAL300000082896 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082896' /scratch/stefan/7930160/working/building/REAL300000082896 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082896 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082896/0 /scratch/stefan/7930160/working/building/REAL300000082896 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/973 `/scratch/stefan/7930160/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(OC)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082896 none CCC1=CC(OC)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [116, 82, 82, 82, 49, 48, 111, 82, 82, 36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 116, 116, 116, 116, 116, 82, 111, 111, 111, 82, 82, 36, 11, 1, 1, 1] 157 rigid atoms, others: [36, 37, 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, 35]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082896 none CCC1=CC(OC)=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 10, 10, 36, 82, 82, 82, 82, 82, 82, 110, 110, 82, 5, 5, 5, 5, 5, 1, 3, 3, 3, 1, 1, 10, 36, 82, 82, 82] 157 rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 9, 10, 33, 28] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082896 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082896 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082896/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082896 Building REAL300000082897 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082897' /scratch/stefan/7930160/working/building/REAL300000082897 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082897 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082897/0 /scratch/stefan/7930160/working/building/REAL300000082897 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/974 `/scratch/stefan/7930160/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C=CC(Br)=C2F)=CC=C1F) `REAL300000082897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082897 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(Br)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 72, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 72, 13, 1, 1, 128, 128] 128 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082897 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(Br)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 11, 47, 47, 128, 128, 128, 94, 128, 128, 128, 128, 1, 1, 1, 1, 1, 11, 47, 128, 93, 1, 1] 128 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082897 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082897 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082897/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082897 Building REAL300000082898 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082898' /scratch/stefan/7930160/working/building/REAL300000082898 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082898 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082898/0 /scratch/stefan/7930160/working/building/REAL300000082898 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/975 `/scratch/stefan/7930160/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082898 none CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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, 201, 133, 102, 133, 85, 85, 85, 85, 41, 41, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 85, 41, 13, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082898 none CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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: [15, 13, 15, 15, 5, 3, 5, 1, 1, 1, 1, 1, 1, 7, 7, 36, 85, 85, 84, 84, 85, 85, 96, 96, 85, 1, 16, 16, 16, 15, 15, 15, 16, 16, 16, 3, 1, 7, 36, 85, 85, 85] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082898 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082898 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082898/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082898 Building REAL300000082899 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082899' /scratch/stefan/7930160/working/building/REAL300000082899 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082899 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082899/0 /scratch/stefan/7930160/working/building/REAL300000082899 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/976 `/scratch/stefan/7930160/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC23CCOCC3)=CC=C1F) `REAL300000082899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082899 none O=C([O-])C1=CC(N=NC2CCCC23CCOCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082899 none O=C([O-])C1=CC(N=NC2CCCC23CCOCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082899 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082899 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082899/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082899 Building REAL300000082900 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082900' /scratch/stefan/7930160/working/building/REAL300000082900 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082900 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082900/0 /scratch/stefan/7930160/working/building/REAL300000082900 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/977 `/scratch/stefan/7930160/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C2C(=N1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082900 none CN1C=C2C(=N1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 4, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1] 22 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 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: REAL300000082900 none CN1C=C2C(=N1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 4, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 38 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082900 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082900 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082900/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082900 Building REAL300000082901 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082901' /scratch/stefan/7930160/working/building/REAL300000082901 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082901 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082901/0 /scratch/stefan/7930160/working/building/REAL300000082901 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/978 `/scratch/stefan/7930160/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F) `REAL300000082901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082901 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 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, 163, 79, 79, 79, 79, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 79, 201, 201, 201, 201, 201, 79, 79, 31, 9, 1, 1, 1, 79] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 486 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082901 none CCOC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 12, 1, 1, 1, 1, 1, 1, 6, 6, 35, 79, 79, 78, 78, 79, 79, 119, 119, 79, 1, 1, 1, 35, 35, 35, 35, 35, 1, 1, 6, 35, 79, 79, 79, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 35, 20, 21, 22, 28, 29] set([0, 1, 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: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082901 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082901 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082901/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082901 Building REAL300000082902 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082902' /scratch/stefan/7930160/working/building/REAL300000082902 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082902 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082902/0 /scratch/stefan/7930160/working/building/REAL300000082902 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/979 `/scratch/stefan/7930160/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082902 none CSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 123, 123, 123, 123, 123, 123, 50, 50, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 174, 174, 174, 123, 123, 123, 123, 50, 50, 50, 11, 1, 1, 1] 174 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 286 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082902 none CSC1=CC=CC=C1C(C)=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 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, 7, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 36, 123, 123, 123, 123, 123, 123, 162, 162, 123, 10, 10, 10, 1, 1, 1, 1, 7, 7, 7, 36, 123, 123, 123] 174 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 373 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082902 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082902 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082902/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082902 Building REAL300000082903 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082903' /scratch/stefan/7930160/working/building/REAL300000082903 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082903 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082903/0 /scratch/stefan/7930160/working/building/REAL300000082903 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/980 `/scratch/stefan/7930160/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2COCC3=CC=CC(Cl)=C32)=CC=C1F) `REAL300000082903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082903 none O=C([O-])C1=CC(NN=C2COCC3=CC=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 46, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 45, 45] 46 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 33]) total number of confs: 67 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: REAL300000082903 none O=C([O-])C1=CC(NN=C2COCC3=CC=CC(Cl)=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 45, 45, 45, 45, 46, 46, 46, 46, 46, 46, 45, 1, 1, 1, 1, 1, 10, 45, 45, 45, 45, 46, 46, 46, 1, 1] 46 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082903 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082903 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082903/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082903 Building REAL300000082904 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082904' /scratch/stefan/7930160/working/building/REAL300000082904 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082904 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082904/0 /scratch/stefan/7930160/working/building/REAL300000082904 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/981 `/scratch/stefan/7930160/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082904 none CCOC(=O)C1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 130, 48, 130, 48, 48, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 48, 48, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 8, 1, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 656 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082904 none CCOC(=O)C1CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 48, 48, 48, 81, 81, 48, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 9, 48, 48, 48, 1, 1, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 41, 42, 43, 44] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082904 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082904 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082904/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082904 Building REAL300000082905 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082905' /scratch/stefan/7930160/working/building/REAL300000082905 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082905 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082905/0 /scratch/stefan/7930160/working/building/REAL300000082905 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/982 `/scratch/stefan/7930160/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=CC=C1F) `REAL300000082905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082905 none O=C([O-])C1=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 75, 62, 62, 36, 36, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 21, 21, 14, 21, 21, 1, 1, 62, 62, 62, 62, 62, 6, 6, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 21, 1, 1, 1, 1, 62, 62] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 46, 44, 23, 24, 45, 47] 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, 37, 38, 39, 40, 41, 42, 43, 48, 49]) 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: REAL300000082905 none O=C([O-])C1=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 2, 2, 17, 62, 62, 62, 62, 113, 113, 113, 188, 201, 201, 195, 201, 201, 62, 57, 1, 1, 1, 1, 1, 17, 17, 62, 62, 62, 62, 62, 188, 188, 201, 201, 201, 201, 201, 62, 62, 62, 62, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 48, 49, 25, 26, 27, 28, 29] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 854 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082905 none O=C([O-])C1=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 170, 170, 70, 21, 20, 20, 20, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 70, 70, 20, 21, 21, 20, 21, 3, 3, 1, 1, 1, 1, 1, 20, 20, 20, 20, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082905 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082905 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082905/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082905 Building REAL300000082906 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082906' /scratch/stefan/7930160/working/building/REAL300000082906 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082906 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082906/0 /scratch/stefan/7930160/working/building/REAL300000082906 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/983 `/scratch/stefan/7930160/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1) `REAL300000082906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082906 none CC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 35, 35, 35, 35, 42, 42, 35, 1, 1, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 35, 35, 35, 1, 1, 1, 1] 93 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 39, 38, 37, 21, 22, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 33, 34, 35]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082906 none CC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 93, 93, 93, 93, 93, 93, 93, 93, 93, 12, 12, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 93, 93, 93, 12, 12, 12, 12] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23] set([6, 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, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082906 none CC1=NOC(C2CCC(N=NC3=CC=C(F)C(C(=O)[O-])=C3)CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 90, 35, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 35, 93, 93, 93, 93, 35, 35, 35, 35, 35, 35, 1, 1, 1, 35, 35, 35, 35] 93 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082906 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082906 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082906/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082906 Building REAL300000082907 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082907' /scratch/stefan/7930160/working/building/REAL300000082907 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082907 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082907/0 /scratch/stefan/7930160/working/building/REAL300000082907 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/984 `/scratch/stefan/7930160/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082907 none CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 28, 28] 29 rigid atoms, others: [40, 41, 42, 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, 38, 39, 43, 44]) total number of confs: 64 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082907 none CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28, 29, 29, 28, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44] set([39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082907 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082907 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082907/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082907 Building REAL300000082908 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082908' /scratch/stefan/7930160/working/building/REAL300000082908 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082908 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082908/0 /scratch/stefan/7930160/working/building/REAL300000082908 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/985 `/scratch/stefan/7930160/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=CC=C1F) `REAL300000082908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082908 none O=C([O-])C1=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 200, 200, 70, 70, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 8, 8, 1, 1, 1, 200, 200] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082908 none O=C([O-])C1=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 42, 200, 200, 200, 200, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 42, 42, 200, 200, 200, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082908 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082908/1 /scratch/stefan/7930160/working/building/REAL300000082908 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/986 `/scratch/stefan/7930160/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=CC=C1F) `REAL300000082908.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082908 none O=C([O-])C1=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 73, 73, 74, 41, 6, 1, 1, 1, 74, 74] 74 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082908 none O=C([O-])C1=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 45, 45, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 11, 45, 74, 74, 74, 1, 1] 74 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082908 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082908 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082908/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082908/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082908 Building REAL300000082909 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082909' /scratch/stefan/7930160/working/building/REAL300000082909 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082909 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082909/0 /scratch/stefan/7930160/working/building/REAL300000082909 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/987 `/scratch/stefan/7930160/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=CS2)=CC=C1F) `REAL300000082909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082909 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [145, 120, 145, 120, 120, 60, 11, 11, 1, 1, 1, 1, 7, 7, 1, 1, 1, 120, 120, 120, 120, 120, 60, 11, 7, 7, 7, 7, 7, 1, 120, 120] 189 rigid atoms, others: [8, 9, 10, 11, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) 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: REAL300000082909 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 11, 55, 55, 120, 120, 189, 189, 120, 120, 120, 1, 1, 1, 1, 1, 11, 55, 189, 189, 189, 189, 189, 120, 1, 1] 189 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082909 none O=C([O-])C1=CC(NN=CC2=C(C3CC3)N=CS2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', '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, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 133, 39, 39, 7, 7, 1, 1, 1, 1, 7, 7, 7, 189, 189, 189, 189, 189, 133, 39, 1, 1, 1, 1, 1, 7, 189, 189] 189 rigid atoms, others: [10, 11, 12, 13, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 412 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082909 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082909 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082909/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082909 Building REAL300000082910 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082910' /scratch/stefan/7930160/working/building/REAL300000082910 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082910 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082910/0 /scratch/stefan/7930160/working/building/REAL300000082910 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/988 `/scratch/stefan/7930160/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=CC=C1F) `REAL300000082910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082910 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [101, 95, 101, 95, 95, 39, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 95, 95, 95, 95, 95, 38, 6, 1, 13, 13, 13, 95, 95] 143 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) 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: REAL300000082910 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 55, 55, 95, 95, 95, 95, 143, 143, 143, 143, 95, 1, 1, 1, 1, 1, 13, 55, 95, 143, 143, 143, 1, 1] 143 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082910 none O=C([O-])C1=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 143, 99, 35, 35, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 143, 143, 143, 143, 143, 99, 34, 13, 1, 1, 1, 143, 143] 143 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 308 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082910 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082910 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082910/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082910 Building REAL300000082911 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082911' /scratch/stefan/7930160/working/building/REAL300000082911 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082911 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082911/0 /scratch/stefan/7930160/working/building/REAL300000082911 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/989 `/scratch/stefan/7930160/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082911 none CCOC1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 103, 76, 76, 76, 76, 76, 76, 76, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 134, 134, 134, 134, 134, 76, 76, 76, 36, 9, 1, 1, 1] 134 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: 351 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: REAL300000082911 none CCOC1=C(Cl)C=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 76, 76, 76, 76, 76, 76, 105, 105, 76, 15, 15, 15, 15, 15, 1, 1, 1, 11, 35, 76, 76, 76] 134 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 302 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082911 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082911 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082911/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082911 Building REAL300000082912 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082912' /scratch/stefan/7930160/working/building/REAL300000082912 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082912 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082912/0 /scratch/stefan/7930160/working/building/REAL300000082912 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/990 `/scratch/stefan/7930160/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1) `REAL300000082912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082912 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [6, 1, 6, 6, 32, 96, 96, 96, 96, 96, 96, 106, 106, 96, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 32, 96, 96, 96, 1, 1, 6, 6, 6, 6, 6, 1, 1] 156 rigid atoms, others: [1, 34, 33, 40, 41, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) 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: REAL300000082912 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 96, 96, 65, 96, 156, 156, 156, 156, 156, 96, 96, 37, 37, 37, 10, 1, 1, 1, 96, 96, 156, 156, 156, 156, 156, 96, 96] 156 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 411 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082912 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 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: [23, 6, 23, 23, 81, 156, 156, 156, 156, 156, 156, 156, 156, 156, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 81, 156, 156, 156, 6, 6, 1, 1, 1, 1, 1, 6, 6] 156 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 333 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082912 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082912 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082912/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082912 Building REAL300000082913 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082913' /scratch/stefan/7930160/working/building/REAL300000082913 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082913 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082913/0 /scratch/stefan/7930160/working/building/REAL300000082913 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/991 `/scratch/stefan/7930160/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082913 none CN1N=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 68, 68, 42, 11, 1, 1, 1] 68 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25]) 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: REAL300000082913 none CN1N=CC(Br)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 10, 10, 43, 68, 68, 68, 68, 68, 68, 68, 68, 68, 2, 2, 2, 1, 10, 43, 68, 68, 68] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082913 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082913 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082913/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082913 Building REAL300000082914 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082914' /scratch/stefan/7930160/working/building/REAL300000082914 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082914 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082914/0 /scratch/stefan/7930160/working/building/REAL300000082914 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/992 `/scratch/stefan/7930160/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082914 none CC1(C)CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 1, 1, 1, 44, 44, 44, 44] 44 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 71 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: REAL300000082914 none CC1(C)CCC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 44, 44, 44, 1, 1, 1, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 38, 39, 40, 41] set([34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082914 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082914 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082914/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082914 Building REAL300000082915 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082915' /scratch/stefan/7930160/working/building/REAL300000082915 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082915 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082915/0 /scratch/stefan/7930160/working/building/REAL300000082915 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/993 `/scratch/stefan/7930160/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082915 none N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 4, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 39, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 1, 1, 1] 40 rigid atoms, others: [37, 38, 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, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082915 none N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 4, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 39, 39, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082915 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082915 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082915/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082915 Building REAL300000082916 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082916' /scratch/stefan/7930160/working/building/REAL300000082916 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082916 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082916/0 /scratch/stefan/7930160/working/building/REAL300000082916 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/994 `/scratch/stefan/7930160/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1) `REAL300000082916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082916 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 28, 28, 69, 69, 69, 69, 69, 69, 91, 91, 69, 1, 1, 1, 1, 1, 2, 2, 9, 11, 12, 11, 1, 5, 5, 5, 5, 69, 69, 69, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 48, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082916 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 69, 69, 69, 69, 113, 113, 201, 201, 201, 201, 69, 35, 35, 35, 35, 1, 1, 1, 69, 69, 69, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 69, 69] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082916 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082916 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082916/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082916 Building REAL300000082917 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082917' /scratch/stefan/7930160/working/building/REAL300000082917 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082917 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082917/0 /scratch/stefan/7930160/working/building/REAL300000082917 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/995 `/scratch/stefan/7930160/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC=C(C(F)(F)F)S2)=CC=C1F) `REAL300000082917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082917 none O=C([O-])C1=CC(N=NCC2=NC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 200, 200, 73, 73, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 200, 200, 200, 200, 200, 8, 8, 1, 200, 200] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27]) 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082917 none O=C([O-])C1=CC(N=NCC2=NC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 51, 200, 200, 200, 200, 201, 201, 201, 200, 1, 1, 1, 1, 1, 51, 51, 200, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082917 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082917/1 /scratch/stefan/7930160/working/building/REAL300000082917 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/996 `/scratch/stefan/7930160/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=C(C(F)(F)F)S2)=CC=C1F) `REAL300000082917.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082917 none O=C([O-])C1=CC(NN=CC2=NC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 40, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 71, 71, 71, 71, 71, 40, 8, 1, 71, 71] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27]) 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: REAL300000082917 none O=C([O-])C1=CC(NN=CC2=NC=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 45, 45, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 12, 45, 71, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082917 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082917 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082917/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082917/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082917 Building REAL300000082918 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082918' /scratch/stefan/7930160/working/building/REAL300000082918 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082918 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082918/0 /scratch/stefan/7930160/working/building/REAL300000082918 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/997 `/scratch/stefan/7930160/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1) `REAL300000082918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082918 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 20, 20, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 3, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 39, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 99 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082918 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 59, 59, 59, 59, 59, 59, 59, 59, 59, 31, 31, 31, 31, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082918 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082918 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082918/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082918 Building REAL300000082919 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082919' /scratch/stefan/7930160/working/building/REAL300000082919 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082919 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082919/0 /scratch/stefan/7930160/working/building/REAL300000082919 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/998 `/scratch/stefan/7930160/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=CC=C1F) `REAL300000082919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082919 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 28, 23, 23, 11, 3, 3, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 33, 33, 33, 1, 1, 23, 23, 23, 23, 23, 11, 3, 1, 1, 33, 33, 33, 33, 1, 1, 23, 23] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38, 39]) 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: REAL300000082919 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 23, 23, 15, 23, 94, 201, 201, 201, 201, 201, 201, 23, 23, 1, 1, 1, 1, 1, 5, 15, 23, 23, 201, 201, 201, 201, 23, 23, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 38, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082919 none O=C([O-])C1=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 129, 69, 69, 33, 33, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 129, 69, 33, 33, 1, 1, 1, 1, 33, 33, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39]) total number of confs: 442 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082919 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082919 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082919/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082919 Building REAL300000082920 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082920' /scratch/stefan/7930160/working/building/REAL300000082920 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082920 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082920/0 /scratch/stefan/7930160/working/building/REAL300000082920 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/999 `/scratch/stefan/7930160/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl) `REAL300000082920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082920 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 40, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 100, 100, 100, 1, 1, 1] 100 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 175 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082920 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 100, 100, 100, 100, 100, 100, 100, 100, 52, 52, 52, 11, 1, 1, 1, 100, 100, 100] 100 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082920 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082920 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082920/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082920 Building REAL300000082921 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082921' /scratch/stefan/7930160/working/building/REAL300000082921 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082921 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082921/0 /scratch/stefan/7930160/working/building/REAL300000082921 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1000 `/scratch/stefan/7930160/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O) `REAL300000082921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082921 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 43, 43, 43, 43, 43, 43, 43, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 50, 50, 50, 43, 43, 24, 8, 1, 1, 1, 86] 100 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 174 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: REAL300000082921 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 26, 43, 43, 43, 43, 43, 43, 50, 50, 43, 1, 1, 4, 4, 4, 1, 1, 8, 26, 43, 43, 43, 2] 100 rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 28, 29] set([0, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082921 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082921/1 /scratch/stefan/7930160/working/building/REAL300000082921 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1001 `/scratch/stefan/7930160/working/3D/1001' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1[O-]) `REAL300000082921.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082921 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 32, 42, 42, 42, 32, 32, 21, 8, 1, 1, 1] 42 rigid atoms, others: [32, 33, 34, 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]) 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: REAL300000082921 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 15, 32, 32, 32, 32, 32, 32, 42, 42, 32, 1, 1, 3, 3, 3, 1, 1, 4, 15, 32, 32, 32] 42 rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 28, 29] set([0, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082921 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082921 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082921/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082921/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082921 Building REAL300000082922 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082922' /scratch/stefan/7930160/working/building/REAL300000082922 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082922 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082922/0 /scratch/stefan/7930160/working/building/REAL300000082922 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1002 `/scratch/stefan/7930160/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082922 none COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 72, 131, 72, 72, 72, 72, 72, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 72, 131, 131, 131, 72, 72, 32, 8, 1, 1, 1, 72] 131 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082922 none COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 72, 72, 72, 72, 72, 72, 94, 94, 72, 1, 13, 13, 13, 1, 1, 10, 35, 72, 72, 72, 1] 131 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082922 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082922 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082922/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082922 Building REAL300000082923 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082923' /scratch/stefan/7930160/working/building/REAL300000082923 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082923 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082923/0 /scratch/stefan/7930160/working/building/REAL300000082923 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1003 `/scratch/stefan/7930160/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082923 none COC(=O)C1=COC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 5, 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, 136, 201, 136, 136, 136, 38, 9, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 136, 201, 201, 201, 136, 38, 38, 38, 38, 1, 1, 1, 136] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082923 none COC(=O)C1=COC(C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 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, 5, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 62, 62, 136, 136, 136, 136, 136, 136, 156, 156, 136, 1, 6, 6, 6, 1, 12, 12, 12, 12, 136, 136, 136, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 22, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082923 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082923/1 /scratch/stefan/7930160/working/building/REAL300000082923 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1004 `/scratch/stefan/7930160/working/3D/1004' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000082923.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082923 none COC(=O)C1=COC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 4, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 89, 155, 89, 89, 89, 37, 37, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 89, 155, 155, 155, 89, 37, 37, 37, 9, 1, 1, 1, 89] 155 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 376 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082923 none COC(=O)C1=COC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 11, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 4, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 10, 37, 89, 89, 88, 88, 89, 89, 102, 102, 89, 1, 12, 12, 12, 1, 11, 11, 11, 37, 89, 89, 89, 1] 155 rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 22, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 253 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082923 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082923 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082923/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082923/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082923 Building REAL300000082924 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082924' /scratch/stefan/7930160/working/building/REAL300000082924 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082924 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082924/0 /scratch/stefan/7930160/working/building/REAL300000082924 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1005 `/scratch/stefan/7930160/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1) `REAL300000082924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082924 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 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, 7, 2, 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: [7, 1, 7, 44, 44, 108, 108, 108, 108, 108, 108, 133, 133, 108, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 7, 7, 7, 108, 108, 108, 1, 1, 13, 13] 201 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 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: REAL300000082924 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 108, 108, 108, 108, 108, 201, 201, 201, 201, 201, 43, 43, 43, 43, 1, 1, 1, 108, 108, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082924 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 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, 7, 2, 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: [44, 13, 44, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 201, 201, 201, 13, 13, 1, 1] 201 rigid atoms, others: [34, 35, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 391 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082924 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082924 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082924/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082924 Building REAL300000082925 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082925' /scratch/stefan/7930160/working/building/REAL300000082925 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082925 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082925/0 /scratch/stefan/7930160/working/building/REAL300000082925 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1006 `/scratch/stefan/7930160/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000082925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082925 none CC(C)C1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 43, 28, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 28, 28, 28, 28, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 10, 1, 1, 1, 28, 28, 28, 28] 43 rigid atoms, others: [35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 136 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: REAL300000082925 none CC(C)C1CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 41, 41, 28, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 6, 28, 28, 28, 1, 1, 1, 1] 43 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 40, 41, 7, 18, 19, 20, 21, 22, 23, 39, 38, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082925 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082925 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082925/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082925 Building REAL300000082926 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082926' /scratch/stefan/7930160/working/building/REAL300000082926 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082926 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082926/0 /scratch/stefan/7930160/working/building/REAL300000082926 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1007 `/scratch/stefan/7930160/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CS1) `REAL300000082926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082926 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 59, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 13, 13, 13, 59, 111, 111, 111, 1, 1] 111 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000082926 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Br)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 111, 111, 111, 111, 111, 49, 49, 49, 10, 1, 1, 1, 111, 111] 111 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 24, 25, 26] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082926 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082926 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082926/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082926 Building REAL300000082927 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082927' /scratch/stefan/7930160/working/building/REAL300000082927 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082927 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082927/0 /scratch/stefan/7930160/working/building/REAL300000082927 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1008 `/scratch/stefan/7930160/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCC(C3CCCCC3)CC2)=CC=C1F) `REAL300000082927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082927 none O=C([O-])C1=CC(N=NC2CCC(C3CCCCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 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: [60, 45, 60, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 45, 45] 101 rigid atoms, others: [42, 43, 7, 8, 9, 10, 11, 12, 45, 44, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) 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: REAL300000082927 none O=C([O-])C1=CC(N=NC2CCC(C3CCCCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 8, 8, 45, 45, 45, 45, 101, 101, 101, 101, 101, 45, 45, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 45, 45, 45, 45, 1, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082927 none O=C([O-])C1=CC(N=NC2CCC(C3CCCCC3)CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 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, 40, 40, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 101, 101, 101, 101, 101, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 101, 101] 101 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082927 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082927 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082927/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082927 Building REAL300000082928 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082928' /scratch/stefan/7930160/working/building/REAL300000082928 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082928 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082928/0 /scratch/stefan/7930160/working/building/REAL300000082928 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1009 `/scratch/stefan/7930160/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(NNC3=CC=C(F)C(C(=O)[O-])=C3)=CSC2=C1) `REAL300000082928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082928 none CC1=CC=C2C(NNC3=CC=C(F)C(C(=O)[O-])=C3)=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 124, 124, 124, 124, 124, 124, 124, 124, 124, 43, 10, 1, 1, 1, 124, 124] 124 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082928 none CC1=CC=C2C(NNC3=CC=C(F)C(C(=O)[O-])=C3)=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 35, 124, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 35, 124, 124, 124, 1, 1] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 18, 19, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082928 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082928 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082928/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082928 Building REAL300000082929 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082929' /scratch/stefan/7930160/working/building/REAL300000082929 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082929 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082929/0 /scratch/stefan/7930160/working/building/REAL300000082929 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1010 `/scratch/stefan/7930160/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl) `REAL300000082929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082929 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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 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, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 112, 112, 112, 112, 112, 112, 112, 112, 49, 13, 1, 1, 1, 112] 112 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082929 none CC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 55, 112, 112, 111, 111, 112, 112, 112, 112, 112, 1, 1, 1, 2, 2, 2, 1, 1, 8, 55, 112, 112, 112, 1] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082929 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082929 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082929/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082929 Building REAL300000082930 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082930' /scratch/stefan/7930160/working/building/REAL300000082930 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082930 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082930/0 /scratch/stefan/7930160/working/building/REAL300000082930 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1011 `/scratch/stefan/7930160/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1) `REAL300000082930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082930 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 12, 1, 12, 12, 75, 155, 155, 155, 155, 155, 155, 159, 159, 155, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 31, 75, 155, 155, 155, 1, 1, 2, 2, 1] 201 rigid atoms, others: [2, 35, 36, 39, 15, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 418 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082930 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 31, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 32, 155, 155, 32, 58, 155, 155, 155, 155, 155, 155, 61, 61, 61, 61, 61, 9, 1, 1, 1, 155, 155, 155, 155, 155] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 586 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082930 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082930 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082930/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082930 Building REAL300000082931 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082931' /scratch/stefan/7930160/working/building/REAL300000082931 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082931 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082931/0 /scratch/stefan/7930160/working/building/REAL300000082931 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1012 `/scratch/stefan/7930160/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082931 none CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 48, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 147, 147, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082931 none CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 21, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21, 5, 5, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 10, 11, 12, 34, 13] set([0, 1, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082931 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082931 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082931/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082931 Building REAL300000082932 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082932' /scratch/stefan/7930160/working/building/REAL300000082932 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082932 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082932/0 /scratch/stefan/7930160/working/building/REAL300000082932 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1013 `/scratch/stefan/7930160/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCN=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)C) `REAL300000082932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082932 none CC(C)(C)OC(=O)N(CCN=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 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, 162, 109, 162, 78, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 109, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 53, 53, 1, 1, 1, 110, 110, 110, 110, 110, 110, 110, 110, 110] 201 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 722 number of broken/clashed sets: 180 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082932 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082932 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082932/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082932 Building REAL300000082933 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082933' /scratch/stefan/7930160/working/building/REAL300000082933 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082933 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082933/0 /scratch/stefan/7930160/working/building/REAL300000082933 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1014 `/scratch/stefan/7930160/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C) `REAL300000082933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082933 none CC(C)C(CN=NC1=CC=C(F)C(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 45, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 50, 140, 195, 195, 201, 201, 201, 201, 45, 45, 45, 45, 45, 45, 45, 43, 20, 20, 1, 1, 1, 50, 49, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 16, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 714 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082933 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082933 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082933/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082933 Building REAL300000082934 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082934' /scratch/stefan/7930160/working/building/REAL300000082934 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082934 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082934/0 /scratch/stefan/7930160/working/building/REAL300000082934 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1015 `/scratch/stefan/7930160/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCC3=CC=C([N+](=O)[O-])C=C32)=CC=C1F) `REAL300000082934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082934 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C([N+](=O)[O-])C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 37, 36]) total number of confs: 56 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: REAL300000082934 none O=C([O-])C1=CC(NN=C2CCCC3=CC=C([N+](=O)[O-])C=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082934 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082934 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082934/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082934 Building REAL300000082935 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082935' /scratch/stefan/7930160/working/building/REAL300000082935 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082935 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082935/0 /scratch/stefan/7930160/working/building/REAL300000082935 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1016 `/scratch/stefan/7930160/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1) `REAL300000082935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082935 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [17, 7, 1, 7, 7, 38, 113, 113, 113, 113, 113, 113, 118, 118, 113, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 38, 113, 113, 113, 1, 1, 1, 1] 125 rigid atoms, others: [32, 33, 2, 35, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 262 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: REAL300000082935 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [88, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 113, 113, 79, 109, 113, 113, 113, 88, 88, 88, 88, 88, 11, 1, 1, 1, 113, 113, 113, 113] 125 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 559 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082935 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082935 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082935/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082935 Building REAL300000082936 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082936' /scratch/stefan/7930160/working/building/REAL300000082936 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082936 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082936/0 /scratch/stefan/7930160/working/building/REAL300000082936 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1017 `/scratch/stefan/7930160/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082936 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [12, 1, 12, 27, 27, 12, 27, 27, 1, 1, 1, 1, 1, 7, 7, 41, 79, 79, 79, 79, 79, 79, 111, 111, 79, 1, 1, 12, 12, 12, 27, 27, 14, 27, 27, 1, 1, 7, 41, 79, 79, 79, 1] 201 rigid atoms, others: [1, 35, 36, 8, 9, 10, 11, 12, 25, 26, 42] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082936 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [7, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 27, 27, 68, 68, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 7, 7, 7, 1, 1, 1, 1, 1, 27, 27, 68, 142, 201, 201, 201, 27] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 34, 33, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082936 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [197, 79, 197, 201, 201, 197, 201, 201, 79, 79, 79, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 197, 197, 197, 201, 201, 199, 201, 201, 79, 79, 27, 9, 1, 1, 1, 79] 201 rigid atoms, others: [39, 40, 41, 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, 42]) total number of confs: 499 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082936 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082936 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082936/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082936 Building REAL300000082937 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082937' /scratch/stefan/7930160/working/building/REAL300000082937 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082937 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082937/0 /scratch/stefan/7930160/working/building/REAL300000082937 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1018 `/scratch/stefan/7930160/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1) `REAL300000082937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082937 none N#CCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 154, 55, 55, 55, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 55, 97, 97, 82, 97, 97, 55, 190, 190, 154, 154, 55, 27, 7, 1, 1, 1, 97, 97, 97, 97] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 835 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082937 none N#CCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 8, 1, 1, 1, 1, 1, 9, 9, 28, 55, 55, 55, 55, 55, 55, 75, 75, 55, 1, 1, 6, 6, 2, 6, 6, 1, 16, 16, 8, 8, 1, 9, 28, 55, 55, 55, 6, 6, 6, 6] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 20, 21, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082937 none N#CCCN1C=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 31, 6, 6, 6, 6, 6, 19, 19, 56, 97, 97, 97, 97, 97, 97, 118, 118, 97, 1, 1, 1, 1, 1, 1, 1, 6, 48, 48, 31, 31, 6, 19, 56, 97, 97, 97, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 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: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082937 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082937 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082937/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082937 Building REAL300000082938 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082938' /scratch/stefan/7930160/working/building/REAL300000082938 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082938 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082938/0 /scratch/stefan/7930160/working/building/REAL300000082938 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1019 `/scratch/stefan/7930160/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=CC=C1F) `REAL300000082938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082938 none O=C([O-])C1=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 37, 54, 37, 37, 12, 12, 1, 1, 1, 1, 1, 6, 22, 45, 45, 23, 45, 45, 1, 36, 36, 37, 37, 37, 1, 1, 1, 1, 22, 22, 45, 45, 45, 45, 45, 1, 1, 37, 37] 201 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 38, 39]) 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: REAL300000082938 none O=C([O-])C1=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 7, 7, 37, 37, 37, 85, 156, 201, 201, 171, 201, 201, 37, 1, 1, 1, 1, 1, 37, 37, 37, 37, 156, 156, 201, 201, 201, 201, 201, 37, 37, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082938 none O=C([O-])C1=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 151, 151, 45, 45, 45, 14, 3, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 45, 45, 45, 45, 3, 3, 1, 1, 1, 1, 1, 45, 45, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082938 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082938 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082938/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082938 Building REAL300000082939 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082939' /scratch/stefan/7930160/working/building/REAL300000082939 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082939 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082939/0 /scratch/stefan/7930160/working/building/REAL300000082939 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1020 `/scratch/stefan/7930160/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C) `REAL300000082939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082939 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 133, 133, 133, 63, 63, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 133, 169, 169, 169, 133, 63, 11, 1, 1, 1, 133, 133, 133, 133, 133] 169 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082939 none COC1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 49, 133, 133, 133, 133, 133, 133, 169, 169, 133, 1, 1, 1, 1, 3, 3, 3, 1, 8, 49, 133, 133, 133, 1, 1, 2, 2, 2] 169 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082939 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082939 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082939/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082939 Building REAL300000082940 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082940' /scratch/stefan/7930160/working/building/REAL300000082940 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082940 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082940/0 /scratch/stefan/7930160/working/building/REAL300000082940 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1021 `/scratch/stefan/7930160/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1) `REAL300000082940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082940 none N#CC1=CC(F)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 74, 44, 74, 74, 74, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 74, 74, 74, 74, 43, 10, 1, 1, 1, 74] 75 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29]) 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: REAL300000082940 none N#CC1=CC(F)=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 11, 46, 75, 75, 75, 1] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082940 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082940 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082940/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082940 Building REAL300000082941 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082941' /scratch/stefan/7930160/working/building/REAL300000082941 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082941 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082941/0 /scratch/stefan/7930160/working/building/REAL300000082941 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1022 `/scratch/stefan/7930160/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(Br)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082941 none CN1N=C(Br)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 102, 102, 102, 102, 53, 13, 1, 1, 1] 102 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082941 none CN1N=C(Br)C=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 8, 53, 102, 102, 101, 101, 102, 102, 102, 102, 102, 2, 2, 2, 1, 8, 53, 102, 102, 102] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082941 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082941 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082941/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082941 Building REAL300000082942 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082942' /scratch/stefan/7930160/working/building/REAL300000082942 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082942 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082942/0 /scratch/stefan/7930160/working/building/REAL300000082942 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1023 `/scratch/stefan/7930160/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1) `REAL300000082942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082942 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 37, 106, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 9, 9, 9, 37, 106, 106, 106, 1, 1, 5, 5, 1, 5, 5] 108 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) 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: REAL300000082942 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 106, 106, 106, 106, 106, 108, 108, 106, 108, 108, 36, 36, 36, 9, 1, 1, 1, 106, 106, 108, 108, 106, 108, 108] 108 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082942 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 5, 13, 13, 39, 108, 108, 108, 108, 108, 108, 108, 108, 108, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 108, 108, 108, 5, 5, 1, 1, 1, 1, 1] 108 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]) total number of confs: 184 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082942 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082942 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082942/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082942 Building REAL300000082943 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082943' /scratch/stefan/7930160/working/building/REAL300000082943 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082943 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082943/0 /scratch/stefan/7930160/working/building/REAL300000082943 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1024 `/scratch/stefan/7930160/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=N1) `REAL300000082943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082943 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 167, 167, 167, 54, 54, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 167, 167, 167, 176, 176, 176, 167, 54, 54, 54, 12, 1, 1, 1, 167, 167] 176 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 260 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082943 none COC1=CC(C(C)=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 13, 13, 13, 65, 167, 167, 167, 167, 167, 167, 170, 170, 167, 1, 1, 1, 3, 3, 3, 1, 13, 13, 13, 65, 167, 167, 167, 1, 1] 176 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082943 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082943 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082943/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082943 Building REAL300000082944 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082944' /scratch/stefan/7930160/working/building/REAL300000082944 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082944 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082944/0 /scratch/stefan/7930160/working/building/REAL300000082944 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1025 `/scratch/stefan/7930160/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(O)C=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O) `REAL300000082944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082944 none CC1=C(O)C=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 536 conformations in input total number of sets (complete confs): 536 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 27, 50, 67, 67, 67, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 67, 67, 67, 67, 134, 67, 134, 27, 8, 1, 1, 1, 134] 536 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 621 number of broken/clashed sets: 286 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082944 none CC1=C(O)C=C(O)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 536 conformations in input total number of sets (complete confs): 536 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 49, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 2, 2, 2, 2, 1, 2, 11, 49, 67, 67, 67, 2] 536 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 163 number of broken/clashed sets: 286 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082944 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082944 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082944/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082944 Building REAL300000082945 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082945' /scratch/stefan/7930160/working/building/REAL300000082945 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082945 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082945/0 /scratch/stefan/7930160/working/building/REAL300000082945 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1026 `/scratch/stefan/7930160/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2COCC3=CC=CC=C32)=CC=C1F) `REAL300000082945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082945 none O=C([O-])C1=CC(NN=C2COCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 40 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 21, 22, 23, 33]) total number of confs: 57 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: REAL300000082945 none O=C([O-])C1=CC(NN=C2COCC3=CC=CC=C32)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 12, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1] 40 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 18, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082945 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082945 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082945/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082945 Building REAL300000082946 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082946' /scratch/stefan/7930160/working/building/REAL300000082946 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082946 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082946/0 /scratch/stefan/7930160/working/building/REAL300000082946 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1027 `/scratch/stefan/7930160/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21) `REAL300000082946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082946 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 1, 1, 1, 37, 37, 37] 37 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 64 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: REAL300000082946 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 37, 37, 37, 1, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 40, 39, 17, 18, 19, 20, 23, 24, 25, 38, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 66 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082946 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082946 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082946/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082946 Building REAL300000082947 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082947' /scratch/stefan/7930160/working/building/REAL300000082947 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082947 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082947/0 /scratch/stefan/7930160/working/building/REAL300000082947 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1028 `/scratch/stefan/7930160/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=C1) `REAL300000082947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082947 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 12, 20, 20, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 20, 39, 97, 185, 185, 185, 185, 185, 20, 31, 31, 31, 20, 20, 12, 7, 1, 1, 1, 97, 97, 185, 185, 185, 185, 20] 201 rigid atoms, others: [36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082947 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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] 0 hydrogens 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, 11, 20, 20, 20, 20, 20, 20, 25, 25, 20, 1, 1, 7, 29, 104, 104, 104, 104, 104, 1, 3, 3, 3, 1, 1, 4, 11, 20, 20, 20, 29, 29, 104, 104, 104, 104, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 45, 19, 20, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082947 none COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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] 0 hydrogens 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, 104, 104, 104, 104, 104, 104, 131, 131, 167, 185, 185, 185, 185, 185, 185, 201, 201, 185, 38, 8, 1, 1, 1, 1, 1, 1, 1, 104, 150, 150, 150, 66, 104, 131, 167, 185, 185, 185, 8, 8, 1, 1, 1, 1, 104] 201 rigid atoms, others: [41, 42, 43, 44, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45]) total number of confs: 639 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082947 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082947 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082947/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082947 Building REAL300000082948 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082948' /scratch/stefan/7930160/working/building/REAL300000082948 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082948 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082948/0 /scratch/stefan/7930160/working/building/REAL300000082948 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1029 `/scratch/stefan/7930160/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082948 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [19, 9, 9, 9, 3, 9, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 65, 65, 65, 65, 65, 65, 109, 109, 65, 19, 19, 19, 9, 8, 9, 9, 1, 1, 10, 34, 65, 65, 65] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) 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: REAL300000082948 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 1, 9, 9, 9, 9, 9, 29, 29, 95, 135, 135, 135, 135, 135, 135, 201, 201, 135, 3, 3, 3, 1, 1, 1, 1, 9, 9, 29, 95, 135, 135, 135] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082948 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 135, 135, 135, 127, 135, 135, 65, 65, 65, 65, 65, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 135, 135, 135, 135, 65, 65, 28, 7, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082948 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082948 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082948/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082948 Building REAL300000082949 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082949' /scratch/stefan/7930160/working/building/REAL300000082949 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082949 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082949/0 /scratch/stefan/7930160/working/building/REAL300000082949 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1030 `/scratch/stefan/7930160/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=CC=C1F) `REAL300000082949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082949 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 38, 53, 38, 38, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 34, 82, 82, 38, 38, 38, 38, 38, 20, 5, 1, 1, 1, 34, 34, 82, 82, 82, 82, 82, 38, 38] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082949 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 21, 21, 38, 38, 38, 38, 38, 38, 38, 91, 168, 201, 201, 1, 1, 1, 1, 1, 6, 21, 38, 38, 38, 168, 168, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 21, 22, 23, 24, 25, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082949 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 168, 113, 113, 82, 82, 82, 82, 82, 82, 82, 46, 10, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 113, 82, 82, 82, 10, 10, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 492 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082949 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082949 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082949/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082949 Building REAL300000082950 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082950' /scratch/stefan/7930160/working/building/REAL300000082950 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082950 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082950/0 /scratch/stefan/7930160/working/building/REAL300000082950 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1031 `/scratch/stefan/7930160/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C) `REAL300000082950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082950 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 27, 84, 84, 84, 84, 84, 84, 115, 115, 84, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 7, 7, 7, 27, 84, 84, 84, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 121 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 287 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082950 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [33, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 84, 84, 73, 84, 84, 84, 90, 121, 121, 121, 34, 34, 34, 9, 1, 1, 1, 84, 84, 84, 84, 121, 121, 121, 121, 121, 121, 121, 121, 121] 121 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082950 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082950 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082950/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082950 Building REAL300000082951 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082951' /scratch/stefan/7930160/working/building/REAL300000082951 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082951 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082951/0 /scratch/stefan/7930160/working/building/REAL300000082951 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1032 `/scratch/stefan/7930160/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082951 none CS(=O)(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 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, 44, 91, 91, 44, 44, 44, 44, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 91, 91, 91, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 44, 44] 91 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082951 none CS(=O)(=O)C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 8, 8, 44, 44, 44, 44, 44, 44, 63, 63, 44, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 1, 1] 91 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 36, 37, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082951 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082951 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082951/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082951 Building REAL300000082952 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082952' /scratch/stefan/7930160/working/building/REAL300000082952 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082952 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082952/0 /scratch/stefan/7930160/working/building/REAL300000082952 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1033 `/scratch/stefan/7930160/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CN=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082952 none N#CC1=CN=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 24, 24, 24, 24, 24, 24, 24, 24, 10, 1, 1, 1] 24 rigid atoms, others: [33, 34, 35, 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]) 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: REAL300000082952 none N#CC1=CN=C2C(=C1)CCCC2=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082952 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082952/1 /scratch/stefan/7930160/working/building/REAL300000082952 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1034 `/scratch/stefan/7930160/working/3D/1034' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CN=C2C(=C1)CCCC2N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082952.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082952 none N#CC1=CN=C2C(=C1)CCCC2N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1] 31 rigid atoms, others: [33, 34, 35, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082952 none N#CC1=CN=C2C(=C1)CCCC2N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32] set([33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082952 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082952 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082952/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082952/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082952 Building REAL300000082953 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082953' /scratch/stefan/7930160/working/building/REAL300000082953 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082953 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082953/0 /scratch/stefan/7930160/working/building/REAL300000082953 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1035 `/scratch/stefan/7930160/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC=C(C3OCCO3)S2)=CC=C1F) `REAL300000082953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(N=NCC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 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, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 83, 122, 83, 83, 47, 47, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 83, 83, 82, 82, 83, 8, 8, 1, 13, 13, 13, 13, 13, 83, 83] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(N=NCC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 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, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 25, 83, 83, 83, 83, 201, 201, 201, 201, 83, 1, 1, 1, 1, 1, 24, 25, 83, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(N=NCC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 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, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 175, 175, 62, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 62, 62, 13, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082953 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082953/1 /scratch/stefan/7930160/working/building/REAL300000082953 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1036 `/scratch/stefan/7930160/working/3D/1036' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=C(C3OCCO3)S2)=CC=C1F) `REAL300000082953.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(NN=CC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 67, 101, 67, 67, 34, 7, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 67, 67, 66, 66, 67, 34, 7, 1, 13, 13, 13, 13, 13, 67, 67] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(NN=CC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens 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, 9, 36, 36, 66, 66, 66, 66, 201, 201, 201, 201, 66, 1, 1, 1, 1, 1, 9, 36, 66, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082953 none O=C([O-])C1=CC(NN=CC2=NC=C(C3OCCO3)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', '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, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 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, 156, 53, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 156, 53, 13, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082953 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082953 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082953/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082953/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082953 Building REAL300000082954 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082954' /scratch/stefan/7930160/working/building/REAL300000082954 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082954 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082954/0 /scratch/stefan/7930160/working/building/REAL300000082954 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1037 `/scratch/stefan/7930160/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN=C(C(F)(F)F)S2)=CC=C1F) `REAL300000082954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082954 none O=C([O-])C1=CC(NN=CC2=CN=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 52, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 111, 111, 111, 111, 111, 52, 9, 1, 111, 111] 111 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082954 none O=C([O-])C1=CC(NN=CC2=CN=C(C(F)(F)F)S2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 55, 55, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 13, 55, 111, 1, 1] 111 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082954 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082954 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082954/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082954 Building REAL300000082955 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082955' /scratch/stefan/7930160/working/building/REAL300000082955 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082955 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082955/0 /scratch/stefan/7930160/working/building/REAL300000082955 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1038 `/scratch/stefan/7930160/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C) `REAL300000082955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082955 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 28, 81, 81, 81, 81, 81, 81, 114, 114, 81, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 7, 7, 7, 28, 81, 81, 81, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 121 rigid atoms, others: [1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 292 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082955 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 81, 81, 81, 66, 81, 81, 81, 88, 121, 121, 121, 32, 32, 32, 8, 1, 1, 1, 81, 81, 81, 121, 121, 121, 121, 121, 121, 121, 121, 121] 121 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 400 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082955 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082955 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082955/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082955 Building REAL300000082956 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082956' /scratch/stefan/7930160/working/building/REAL300000082956 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082956 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082956/0 /scratch/stefan/7930160/working/building/REAL300000082956 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1039 `/scratch/stefan/7930160/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082956 none CN1N=CC=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 35, 35, 35, 35, 35, 35, 53, 53, 35, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 1, 1] 68 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 41, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 37, 38, 39]) total number of confs: 121 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: REAL300000082956 none CN1N=CC=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 6, 6, 26, 26, 68, 68, 68, 68, 68, 68, 68, 68, 68, 6, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 68, 68, 68, 6, 6] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082956 none CN1N=CC=C1C1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 35, 35, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 68, 68, 68, 68, 68, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 35, 35] 68 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40, 41]) total number of confs: 134 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082956 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082956 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082956/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082956 Building REAL300000082957 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082957' /scratch/stefan/7930160/working/building/REAL300000082957 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082957 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082957/0 /scratch/stefan/7930160/working/building/REAL300000082957 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1040 `/scratch/stefan/7930160/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=NC=C3C=C2)=CC=C1F) `REAL300000082957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082957 none O=C([O-])C1=CC(NN=CC2=CC3=CC=NC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 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, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 50, 10, 1, 1, 1, 1, 1, 1, 122, 122] 122 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) 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: REAL300000082957 none O=C([O-])C1=CC(NN=CC2=CC3=CC=NC=C3C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 54, 54, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 13, 54, 122, 122, 122, 122, 122, 122, 1, 1] 122 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082957 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082957 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082957/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082957 Building REAL300000082958 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082958' /scratch/stefan/7930160/working/building/REAL300000082958 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082958 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082958/0 /scratch/stefan/7930160/working/building/REAL300000082958 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1041 `/scratch/stefan/7930160/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082958 none CCC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 80, 80, 80, 30, 80, 80, 80, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 118, 118, 118, 118, 118, 80, 55, 80, 30, 10, 1, 1, 1] 118 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082958 none CCC1=CC=CC(Cl)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 80, 80, 80, 80, 80, 80, 93, 93, 80, 5, 5, 5, 5, 5, 1, 1, 1, 7, 30, 80, 80, 80] 118 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082958 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082958 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082958/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082958 Building REAL300000082959 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082959' /scratch/stefan/7930160/working/building/REAL300000082959 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082959 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082959/0 /scratch/stefan/7930160/working/building/REAL300000082959 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1042 `/scratch/stefan/7930160/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C(F)F)C=C2)=CC=C1F) `REAL300000082959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082959 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 77, 101, 77, 77, 30, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 77, 77, 77, 77, 77, 30, 6, 1, 1, 12, 1, 1, 77, 77] 132 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 25, 26, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082959 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)F)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 10, 54, 55, 77, 77, 55, 55, 130, 130, 77, 77, 1, 1, 1, 1, 1, 10, 54, 77, 77, 130, 77, 77, 1, 1] 132 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082959 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082959 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082959/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082959 Building REAL300000082960 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082960' /scratch/stefan/7930160/working/building/REAL300000082960 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082960 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082960/0 /scratch/stefan/7930160/working/building/REAL300000082960 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1043 `/scratch/stefan/7930160/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C) `REAL300000082960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082960 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 45, 163, 163, 163, 163, 163, 163, 183, 183, 163, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 45, 163, 163, 163, 1, 4, 4, 2, 2, 2, 1, 2, 2, 2] 197 rigid atoms, others: [1, 33, 39, 14, 15, 16, 17, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 363 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082960 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 163, 163, 163, 197, 197, 197, 102, 120, 163, 163, 163, 60, 60, 60, 12, 1, 1, 1, 163, 197, 197, 163, 163, 163, 163, 163, 163, 163] 197 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 857 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082960 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082960 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082960/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082960 Building REAL300000082961 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082961' /scratch/stefan/7930160/working/building/REAL300000082961 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082961 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082961/0 /scratch/stefan/7930160/working/building/REAL300000082961 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1044 `/scratch/stefan/7930160/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1) `REAL300000082961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082961 none CC(C)CC1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 30, 30] 30 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 72 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: REAL300000082961 none CC(C)CC1CCCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 1, 1] 30 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 42, 43, 35, 21, 36, 38, 37, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082961 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082961 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082961/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082961 Building REAL300000082962 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082962' /scratch/stefan/7930160/working/building/REAL300000082962 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082962 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082962/0 /scratch/stefan/7930160/working/building/REAL300000082962 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1045 `/scratch/stefan/7930160/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Br) `REAL300000082962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082962 none CC1=NN(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 113, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 113, 113, 113, 113, 113, 113, 113, 113, 56, 11, 1, 1, 1] 113 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000082962 none CC1=NN(C)C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 12, 12, 66, 113, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 2, 2, 2, 2, 2, 2, 12, 66, 113, 113, 113] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082962 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082962 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082962/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082962 Building REAL300000082963 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082963' /scratch/stefan/7930160/working/building/REAL300000082963 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082963 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082963/0 /scratch/stefan/7930160/working/building/REAL300000082963 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1046 `/scratch/stefan/7930160/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C1=CC=CC=C1)C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082963 none COC(C1=CC=CC=C1)C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [193, 179, 63, 179, 182, 182, 179, 182, 182, 8, 63, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 193, 193, 193, 179, 182, 182, 179, 182, 182, 63, 63, 63, 63, 1, 1, 1] 196 rigid atoms, others: [36, 37, 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, 35]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082963 none COC(C1=CC=CC=C1)C(C)N=NC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 72, 72, 182, 182, 182, 182, 182, 182, 196, 196, 182, 5, 5, 5, 3, 1, 1, 1, 1, 1, 12, 12, 12, 12, 182, 182, 182] 196 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082963 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082963 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082963/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082963 Building REAL300000082964 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082964' /scratch/stefan/7930160/working/building/REAL300000082964 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082964 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082964/0 /scratch/stefan/7930160/working/building/REAL300000082964 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1047 `/scratch/stefan/7930160/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=CC=C1F) `REAL300000082964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082964 none O=C([O-])C1=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 70, 75, 70, 70, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 70, 70, 69, 69, 70, 29, 11, 1, 1, 6, 6, 3, 6, 6, 70, 70] 75 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000082964 none O=C([O-])C1=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 21, 21, 70, 70, 70, 70, 70, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 8, 21, 70, 70, 75, 75, 75, 75, 75, 1, 1] 75 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082964 none O=C([O-])C1=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 39, 21, 21, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 39, 21, 6, 6, 1, 1, 1, 1, 1, 75, 75] 75 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 158 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082964 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082964/1 /scratch/stefan/7930160/working/building/REAL300000082964 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1048 `/scratch/stefan/7930160/working/3D/1048' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=CC=C1F) `REAL300000082964.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082964 none O=C([O-])C1=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 152, 201, 152, 152, 55, 55, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 152, 152, 152, 152, 152, 7, 7, 1, 1, 6, 6, 2, 6, 6, 152, 152] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082964 none O=C([O-])C1=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 52, 152, 152, 152, 152, 152, 201, 201, 161, 201, 201, 1, 1, 1, 1, 1, 52, 52, 152, 152, 201, 201, 199, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082964 none O=C([O-])C1=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 103, 103, 20, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 20, 20, 6, 6, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 319 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082964 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082964 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082964/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082964/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082964 Building REAL300000082965 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082965' /scratch/stefan/7930160/working/building/REAL300000082965 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082965 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082965/0 /scratch/stefan/7930160/working/building/REAL300000082965 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1049 `/scratch/stefan/7930160/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1C) `REAL300000082965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082965 none COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 73, 133, 73, 73, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 73, 73, 73, 133, 133, 133, 73, 31, 9, 1, 1, 1, 73, 73, 73, 73] 133 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) 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: REAL300000082965 none COC(=O)C1=CC(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 35, 73, 73, 73, 73, 73, 73, 82, 82, 73, 1, 1, 1, 13, 13, 13, 1, 6, 34, 73, 73, 73, 1, 2, 2, 2] 133 rigid atoms, others: [32, 2, 4, 5, 6, 7, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082965 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082965 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082965/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082965 Building REAL300000082966 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082966' /scratch/stefan/7930160/working/building/REAL300000082966 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082966 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082966/0 /scratch/stefan/7930160/working/building/REAL300000082966 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1050 `/scratch/stefan/7930160/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Br)=CC=C21) `REAL300000082966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082966 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 1, 1, 1, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 56 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: REAL300000082966 none CC1(C)CC(=NNC2=CC=C(F)C(C(=O)[O-])=C2)C2=CC(Br)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 31, 31, 31, 1, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 36, 38, 37, 30, 31] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082966 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082966 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082966/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082966 Building REAL300000082967 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082967' /scratch/stefan/7930160/working/building/REAL300000082967 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082967 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082967/0 /scratch/stefan/7930160/working/building/REAL300000082967 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1051 `/scratch/stefan/7930160/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C=CC(O)=C2F)=CC=C1F) `REAL300000082967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082967 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(O)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 12, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 63, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 63, 13, 1, 1, 2, 107, 107] 214 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) 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: REAL300000082967 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC(O)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 12, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 45, 45, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 11, 45, 107, 107, 214, 1, 1] 214 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: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082967 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082967 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082967/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082967 Building REAL300000082968 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082968' /scratch/stefan/7930160/working/building/REAL300000082968 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082968 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082968/0 /scratch/stefan/7930160/working/building/REAL300000082968 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1052 `/scratch/stefan/7930160/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)N1C=NC=N1) `REAL300000082968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082968 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [25, 12, 28, 82, 82, 143, 143, 143, 143, 143, 143, 143, 143, 143, 1, 12, 12, 1, 1, 1, 1, 1, 28, 28, 28, 28, 143, 143, 143, 12, 12, 12, 12, 12, 12, 1, 1] 143 rigid atoms, others: [35, 36, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082968 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)(C)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 80, 84, 89, 143, 143, 143, 143, 30, 30, 30, 30, 1, 1, 1, 89, 89, 89, 89, 89, 89, 143, 143] 143 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082968 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082968 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082968/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082968 Building REAL300000082969 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082969' /scratch/stefan/7930160/working/building/REAL300000082969 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082969 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082969/0 /scratch/stefan/7930160/working/building/REAL300000082969 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1053 `/scratch/stefan/7930160/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1C) `REAL300000082969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082969 none COC(=O)CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 111, 201, 40, 40, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 201, 201, 201, 111, 111, 40, 40, 40, 40, 40, 40, 1, 1, 1, 40, 40, 40, 40] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082969 none COC(=O)CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 9, 41, 1, 1, 1, 1, 1, 1, 8, 8, 40, 40, 40, 40, 40, 40, 67, 67, 40, 1, 1, 41, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 40, 40, 40, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 37, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 34, 35, 36, 38, 39, 40]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082969 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082969 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082969/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082969 Building REAL300000082970 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082970' /scratch/stefan/7930160/working/building/REAL300000082970 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082970 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082970/0 /scratch/stefan/7930160/working/building/REAL300000082970 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1054 `/scratch/stefan/7930160/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=N1) `REAL300000082970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082970 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 56, 153, 153, 153, 153, 153, 153, 177, 177, 153, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 11, 56, 153, 153, 153, 1, 1, 3] 177 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 36, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082970 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 3, 20, 20, 86, 177, 177, 177, 177, 177, 177, 177, 177, 177, 3, 3, 1, 1, 2, 2, 2, 1, 3, 3, 20, 86, 177, 177, 177, 3, 3, 1] 177 rigid atoms, others: [0, 1, 2, 3, 4, 38, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082970 none CN1C=C(C2=CC=C(C=NNC3=CC=C(F)C(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 153, 121, 153, 153, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 153, 153, 177, 177, 177, 177, 177, 177, 153, 153, 66, 13, 1, 1, 1, 153, 153, 177] 177 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 433 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082970 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082970 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082970/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082970 Building REAL300000082971 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082971' /scratch/stefan/7930160/working/building/REAL300000082971 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082971 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082971/0 /scratch/stefan/7930160/working/building/REAL300000082971 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1055 `/scratch/stefan/7930160/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1) `REAL300000082971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082971 none CC(O)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 471 conformations in input total number of sets (complete confs): 471 using faster count positions algorithm for large data unique positions, atoms: [157, 70, 157, 70, 70, 70, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 70, 157, 157, 157, 157, 471, 70, 30, 9, 1, 1, 1] 471 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 987 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082971 none CC(O)C1=NC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 471 conformations in input total number of sets (complete confs): 471 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 35, 70, 70, 70, 70, 70, 70, 92, 92, 70, 1, 12, 12, 12, 12, 36, 1, 6, 34, 70, 70, 70] 471 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 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/7930160/working/building/REAL300000082971 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082971 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082971/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082971 Building REAL300000082972 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082972' /scratch/stefan/7930160/working/building/REAL300000082972 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082972 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082972/0 /scratch/stefan/7930160/working/building/REAL300000082972 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1056 `/scratch/stefan/7930160/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=CC=C1F) `REAL300000082972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082972 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 36, 45, 36, 36, 19, 6, 6, 1, 1, 1, 1, 1, 1, 12, 74, 74, 74, 74, 74, 1, 36, 36, 36, 36, 36, 18, 6, 1, 1, 74, 74, 74, 74, 36, 36] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082972 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 36, 36, 36, 36, 137, 201, 201, 201, 201, 201, 36, 1, 1, 1, 1, 1, 5, 23, 36, 36, 201, 201, 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: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082972 none O=C([O-])C1=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', '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, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 182, 108, 108, 74, 74, 74, 74, 12, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 182, 108, 74, 74, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082972 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082972 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082972/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082972 Building REAL300000082973 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082973' /scratch/stefan/7930160/working/building/REAL300000082973 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082973 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082973/0 /scratch/stefan/7930160/working/building/REAL300000082973 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1057 `/scratch/stefan/7930160/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2Br)=CC=C1F) `REAL300000082973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082973 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 116, 117, 116, 116, 65, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 65, 11, 1, 1, 1, 116, 116] 117 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082973 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2Br)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 48, 48, 116, 116, 116, 66, 116, 116, 116, 1, 1, 1, 1, 1, 12, 48, 116, 92, 116, 1, 1] 117 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: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082973 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082973 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082973/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082973 Building REAL300000082974 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082974' /scratch/stefan/7930160/working/building/REAL300000082974 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082974 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082974/0 /scratch/stefan/7930160/working/building/REAL300000082974 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1058 `/scratch/stefan/7930160/working/3D/1058' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2) `REAL300000082974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082974 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [117, 61, 61, 61, 61, 61, 61, 61, 61, 114, 61, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 61, 117, 117, 117, 61, 61, 114, 114, 114, 10, 1, 1, 1, 61, 61, 61, 61] 127 rigid atoms, others: [34, 35, 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, 33, 37, 38, 39, 40]) 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: REAL300000082974 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 9, 61, 61, 61, 61, 61, 61, 104, 104, 61, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 9, 61, 61, 61, 1, 1, 1, 1] 127 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 40, 23, 24, 39, 38, 28, 29, 37] set([0, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082974 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082974 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082974/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082974 Building REAL300000082975 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082975' /scratch/stefan/7930160/working/building/REAL300000082975 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082975 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082975/0 /scratch/stefan/7930160/working/building/REAL300000082975 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1059 `/scratch/stefan/7930160/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=N2)=CC=C1F) `REAL300000082975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082975 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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, 53, 54, 53, 53, 28, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 53, 53, 53, 53, 53, 28, 6, 1, 1, 1, 53, 53] 54 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082975 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 42, 42, 53, 53, 53, 53, 54, 54, 53, 53, 1, 1, 1, 1, 1, 10, 42, 53, 53, 53, 1, 1] 54 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082975 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082975 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082975/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082975 Building REAL300000082976 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082976' /scratch/stefan/7930160/working/building/REAL300000082976 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082976 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082976/0 /scratch/stefan/7930160/working/building/REAL300000082976 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1060 `/scratch/stefan/7930160/working/3D/1060' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1) `REAL300000082976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082976 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 36, 36, 86, 86, 86, 86, 86, 86, 107, 107, 86, 1, 1, 1, 1, 3, 3, 9, 10, 10, 10, 1, 6, 6, 6, 6, 86, 86, 86, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 44, 45, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082976 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 86, 86, 86, 129, 129, 201, 201, 201, 201, 86, 42, 42, 42, 42, 1, 1, 1, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 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: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082976 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082976 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082976/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082976 Building REAL300000082977 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082977' /scratch/stefan/7930160/working/building/REAL300000082977 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082977 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082977/0 /scratch/stefan/7930160/working/building/REAL300000082977 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1061 `/scratch/stefan/7930160/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(N2C=NC=N2)C1) `REAL300000082977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082977 none CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(N2C=NC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 56, 56, 56, 56, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 56, 56, 31, 31] 56 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082977 none CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(N2C=NC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 45, 45, 31, 1, 1, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 31, 31, 31, 1, 6, 6, 1, 1] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 39, 17, 18, 23, 36, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 33, 34, 35, 37, 38]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082977 none CC1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)C(N2C=NC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 6, 24, 24, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 56, 56, 56, 6, 1, 1, 6, 6] 56 rigid atoms, others: [37, 38, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082977 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082977 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082977/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082977 Building REAL300000082978 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082978' /scratch/stefan/7930160/working/building/REAL300000082978 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082978 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082978/0 /scratch/stefan/7930160/working/building/REAL300000082978 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1062 `/scratch/stefan/7930160/working/3D/1062' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(F)(F)F)=C1) `REAL300000082978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082978 none CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [94, 38, 94, 38, 66, 66, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 66, 66, 66, 66, 94, 94, 94, 94, 94, 94, 66, 66, 38, 11, 1, 1, 1, 66] 104 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 339 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082978 none CN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 21, 66, 66, 66, 66, 66, 66, 104, 104, 66, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 21, 66, 66, 66, 1] 104 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 7, 20, 21, 25, 39] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082978 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082978 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082978/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082978 Building REAL300000082979 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082979' /scratch/stefan/7930160/working/building/REAL300000082979 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082979 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082979/0 /scratch/stefan/7930160/working/building/REAL300000082979 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1063 `/scratch/stefan/7930160/working/3D/1063' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=CC=C1F) `REAL300000082979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082979 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 104, 115, 104, 104, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 104, 104, 104, 104, 104, 38, 11, 1, 1, 5, 5, 4, 5, 5, 104, 104] 115 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082979 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 9, 42, 42, 104, 104, 104, 104, 104, 115, 115, 114, 115, 115, 1, 1, 1, 1, 1, 9, 42, 104, 104, 115, 115, 115, 115, 115, 1, 1] 115 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082979 none O=C([O-])C1=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 14, 14, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 46, 14, 5, 5, 1, 1, 1, 1, 1, 115, 115] 115 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082979 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082979 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082979/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082979 Building REAL300000082980 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082980' /scratch/stefan/7930160/working/building/REAL300000082980 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082980 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082980/0 /scratch/stefan/7930160/working/building/REAL300000082980 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1064 `/scratch/stefan/7930160/working/3D/1064' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC) `REAL300000082980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082980 none COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 99, 99, 99, 99, 58, 33, 58, 6, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 99, 99, 99, 191, 178, 178, 178, 99, 99, 58, 58, 58, 58, 33, 33, 33, 33, 1, 1, 1, 99, 191, 191, 191] 201 rigid atoms, others: [39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082980 none COC1=CC=C(C(C)C(C)N=NC2=CC=C(F)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7] 0 hydrogens 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, 8, 8, 43, 43, 99, 99, 99, 99, 99, 99, 148, 148, 99, 1, 1, 1, 3, 3, 3, 3, 1, 1, 2, 3, 3, 3, 8, 9, 9, 9, 99, 99, 99, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 22, 23, 24, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082980 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082980 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082980/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082980 Building REAL300000082981 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082981' /scratch/stefan/7930160/working/building/REAL300000082981 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082981 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082981/0 /scratch/stefan/7930160/working/building/REAL300000082981 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1065 `/scratch/stefan/7930160/working/3D/1065' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000082981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082981 none CCC1=CC=CC(F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 77, 77, 77, 33, 77, 77, 77, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 95, 95, 95, 95, 95, 77, 76, 77, 27, 6, 1, 1, 1] 95 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082981 none CCC1=CC=CC(F)=C1C=NNC1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 38, 77, 77, 77, 77, 77, 77, 91, 91, 77, 5, 5, 5, 5, 5, 1, 1, 1, 10, 38, 77, 77, 77] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082981 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082981 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082981/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082981 Building REAL300000082982 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082982' /scratch/stefan/7930160/working/building/REAL300000082982 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082982 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082982/0 /scratch/stefan/7930160/working/building/REAL300000082982 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1066 `/scratch/stefan/7930160/working/3D/1066' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1) `REAL300000082982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082982 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [14, 4, 14, 76, 76, 200, 200, 200, 200, 200, 200, 200, 200, 200, 1, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 200, 200, 200, 4, 4, 4, 4, 1, 1, 1, 1] 200 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 306 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: REAL300000082982 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 164, 171, 200, 200, 200, 200, 200, 200, 59, 59, 59, 59, 1, 1, 1, 171, 171, 171, 171, 200, 200, 200, 200] 200 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 725 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082982 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082982 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082982/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082982 Building REAL300000082983 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082983' /scratch/stefan/7930160/working/building/REAL300000082983 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082983 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082983/0 /scratch/stefan/7930160/working/building/REAL300000082983 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1067 `/scratch/stefan/7930160/working/3D/1067' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2) `REAL300000082983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082983 none CC1=CC(Br)=CC2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 41, 41, 41, 41, 41, 41, 9, 1, 1, 1, 41, 41, 41, 41] 41 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, 32, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082983 none CC1=CC(Br)=CC2=C1C(=NNC1=CC=C(F)C(C(=O)[O-])=C1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 40, 40, 41, 41, 41, 41, 41, 1, 1, 2, 2, 2, 1, 1, 9, 41, 41, 41, 1, 1, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 21, 22, 26, 27, 35] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082983 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082983 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082983/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082983 Building REAL300000082984 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082984' /scratch/stefan/7930160/working/building/REAL300000082984 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082984 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082984/0 /scratch/stefan/7930160/working/building/REAL300000082984 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1068 `/scratch/stefan/7930160/working/3D/1068' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CC(C)(C)C2=C1) `REAL300000082984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082984 none COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CC(C)(C)C2=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 28, 28, 28, 28, 28, 28, 50, 50, 50, 28, 28, 10, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 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: REAL300000082984 none COC1=CC=C2C(=NNC3=CC=C(F)C(C(=O)[O-])=C3)CC(C)(C)C2=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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 50, 50, 28, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 6, 28, 28, 28, 1, 1, 2, 2, 2, 2, 2, 2, 1] 50 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 42, 34, 19, 20, 21, 22, 23, 24, 28, 29, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082984 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082984 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082984/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082984 Building REAL300000082985 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082985' /scratch/stefan/7930160/working/building/REAL300000082985 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082985 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082985/0 /scratch/stefan/7930160/working/building/REAL300000082985 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1069 `/scratch/stefan/7930160/working/3D/1069' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O) `REAL300000082985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082985 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 64, 126, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 126, 126, 126, 1, 1, 2] 252 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 241 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: REAL300000082985 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 126, 126, 126, 102, 126, 126, 126, 126, 47, 47, 47, 10, 1, 1, 1, 126, 126, 252] 252 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 554 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082985 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082985/1 /scratch/stefan/7930160/working/building/REAL300000082985 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1070 `/scratch/stefan/7930160/working/3D/1070' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-]) `REAL300000082985.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082985 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 37, 37, 37, 1, 1] 37 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082985 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 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: [26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 26, 8, 1, 1, 1, 37, 37] 37 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082985 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082985 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082985/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082985/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082985 Building REAL300000082986 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082986' /scratch/stefan/7930160/working/building/REAL300000082986 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082986 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082986/0 /scratch/stefan/7930160/working/building/REAL300000082986 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1071 `/scratch/stefan/7930160/working/3D/1071' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082986 none CC(C)N(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 53, 183, 53, 53, 53, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 53, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 53, 53, 20, 5, 1, 1, 1, 53] 201 rigid atoms, others: [38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 522 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: REAL300000082986 none CC(C)N(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 12, 36, 1, 12, 1, 1, 1, 1, 1, 6, 6, 28, 53, 53, 53, 53, 53, 53, 77, 77, 53, 1, 1, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 1, 1, 6, 27, 53, 53, 53, 1] 201 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 35, 41, 22, 23] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 332 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082986 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082986 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082986/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082986 Building REAL300000082987 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082987' /scratch/stefan/7930160/working/building/REAL300000082987 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082987 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082987/0 /scratch/stefan/7930160/working/building/REAL300000082987 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1072 `/scratch/stefan/7930160/working/3D/1072' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(F)(F)CC1) `REAL300000082987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082987 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 62, 62, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1] 130 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082987 none CC(N=NC1=CC=C(F)C(C(=O)[O-])=C1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [65, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 65, 127, 130, 130, 130, 130, 130, 127, 65, 65, 65, 65, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 130] 130 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 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: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082987 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082987 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082987/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082987 Building REAL300000082988 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082988' /scratch/stefan/7930160/working/building/REAL300000082988 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082988 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082988/0 /scratch/stefan/7930160/working/building/REAL300000082988 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1073 `/scratch/stefan/7930160/working/3D/1073' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=C(F)C=C3N2)=CC=C1F) `REAL300000082988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082988 none O=C([O-])C1=CC(NN=CC2=CC3=CC=C(F)C=C3N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 66, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 66, 32, 6, 1, 1, 1, 1, 1, 67, 67] 67 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082988 none O=C([O-])C1=CC(NN=CC2=CC3=CC=C(F)C=C3N2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 50, 50, 66, 66, 66, 66, 66, 67, 67, 66, 52, 1, 1, 1, 1, 1, 10, 50, 66, 66, 66, 67, 67, 1, 1] 67 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082988 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082988 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082988/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082988 Building REAL300000082989 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082989' /scratch/stefan/7930160/working/building/REAL300000082989 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082989 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082989/0 /scratch/stefan/7930160/working/building/REAL300000082989 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1074 `/scratch/stefan/7930160/working/3D/1074' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=CC=C1F) `REAL300000082989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082989 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 106, 106, 106, 106, 106, 44, 7, 1, 1, 1, 106, 106] 106 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082989 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 71, 71, 106, 106, 95, 98, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 13, 71, 106, 106, 106, 1, 1] 106 rigid atoms, others: [32, 1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082989 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082989 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082989/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082989 Building REAL300000082990 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082990' /scratch/stefan/7930160/working/building/REAL300000082990 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082990 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082990/0 /scratch/stefan/7930160/working/building/REAL300000082990 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1075 `/scratch/stefan/7930160/working/3D/1075' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=CC=C1F) `REAL300000082990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082990 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 59, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 125, 125, 126, 59, 10, 1, 1, 1, 126, 126] 126 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082990 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 13, 55, 55, 126, 126, 102, 126, 126, 126, 126, 1, 1, 1, 1, 1, 13, 55, 126, 126, 126, 1, 1] 126 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: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082990 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082990 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082990/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082990 Building REAL300000082991 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082991' /scratch/stefan/7930160/working/building/REAL300000082991 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082991 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082991/0 /scratch/stefan/7930160/working/building/REAL300000082991 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1076 `/scratch/stefan/7930160/working/3D/1076' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1) `REAL300000082991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082991 none COCCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 153, 93, 29, 93, 29, 29, 29, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 29, 201, 201, 201, 195, 195, 153, 153, 93, 93, 93, 29, 29, 12, 4, 1, 1, 1, 29] 201 rigid atoms, others: [39, 40, 41, 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, 35, 36, 37, 38, 42]) total number of confs: 793 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: REAL300000082991 none COCCN(C)C1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 34, 24, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 16, 29, 29, 29, 29, 29, 29, 38, 38, 29, 1, 1, 49, 49, 49, 34, 34, 24, 24, 10, 10, 10, 1, 1, 7, 16, 29, 29, 29, 1] 201 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 23, 24, 36, 42] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 268 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082991 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082991 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082991/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082991 Building REAL300000082992 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082992' /scratch/stefan/7930160/working/building/REAL300000082992 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000082992 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082992/0 /scratch/stefan/7930160/working/building/REAL300000082992 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1077 `/scratch/stefan/7930160/working/3D/1077' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=CC=C1F) `REAL300000082992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082992 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 67, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 67, 13, 2, 1, 1, 107, 107] 214 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 225 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: REAL300000082992 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 214 conformations in input total number of sets (complete confs): 214 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 42, 42, 107, 107, 107, 71, 107, 107, 107, 107, 1, 1, 1, 1, 1, 11, 42, 214, 107, 107, 1, 1] 214 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: 504 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082992 /scratch/stefan/7930160/working /scratch/stefan/7930160 mkdir: created directory `1' /scratch/stefan/7930160/working/building/REAL300000082992/1 /scratch/stefan/7930160/working/building/REAL300000082992 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 1 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1078 `/scratch/stefan/7930160/working/3D/1078' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=CC=C1F) `REAL300000082992.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000082992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082992 none O=C([O-])C1=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 16, 4, 1, 1, 23, 23] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 27, 28]) 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: REAL300000082992 none O=C([O-])C1=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 17, 17, 23, 23, 23, 17, 23, 23, 23, 23, 1, 1, 1, 1, 1, 7, 17, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082992 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082992 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 1: /scratch/stefan/7930160/working/building/REAL300000082992/1.* 0: /scratch/stefan/7930160/working/building/REAL300000082992/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082992 Building REAL300000082993 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082993' /scratch/stefan/7930160/working/building/REAL300000082993 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082993 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082993/0 /scratch/stefan/7930160/working/building/REAL300000082993 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1079 `/scratch/stefan/7930160/working/3D/1079' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CC=C3)C2)=CC=C1F) `REAL300000082993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082993 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 49, 75, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 49, 49] 75 rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 12, 13, 19, 39, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082993 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 75, 75, 50, 75, 75, 49, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 75, 75, 66, 75, 75, 49, 49, 1, 1] 75 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082993 none O=C([O-])C1=CC(N=NC2CCCC(C3=CC=CC=C3)C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 75, 75, 75, 75, 75, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 75, 75] 75 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082993 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082993 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082993/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082993 Building REAL300000082994 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082994' /scratch/stefan/7930160/working/building/REAL300000082994 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082994 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082994/0 /scratch/stefan/7930160/working/building/REAL300000082994 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1080 `/scratch/stefan/7930160/working/3D/1080' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000082994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082994 none COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 177, 201, 96, 31, 20, 44, 44, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 201, 201, 201, 177, 177, 44, 44, 20, 7, 1, 1, 1, 44] 201 rigid atoms, others: [37, 38, 39, 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, 35, 36, 40]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082994 none COC(=O)COC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 17, 40, 5, 1, 1, 1, 1, 1, 1, 7, 7, 24, 44, 44, 44, 44, 44, 44, 59, 59, 44, 1, 1, 1, 2, 2, 40, 40, 40, 17, 17, 1, 1, 7, 24, 44, 44, 44, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 40, 23, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082994 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082994 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082994/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082994 Building REAL300000082995 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082995' /scratch/stefan/7930160/working/building/REAL300000082995 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082995 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082995/0 /scratch/stefan/7930160/working/building/REAL300000082995 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1081 `/scratch/stefan/7930160/working/3D/1081' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1) `REAL300000082995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082995 none COC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 34, 83, 34, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 34, 83, 83, 83, 34, 34, 34, 34, 34, 34, 1, 1, 1, 34, 34, 34, 34] 83 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082995 none COC(=O)C1CCC(N=NC2=CC=C(F)C(C(=O)[O-])=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 5, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 34, 43, 43, 34, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 34, 34, 34, 1, 1, 1, 1] 83 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 37, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([0, 1, 3, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082995 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082995 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082995/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082995 Building REAL300000082996 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082996' /scratch/stefan/7930160/working/building/REAL300000082996 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082996 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082996/0 /scratch/stefan/7930160/working/building/REAL300000082996 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1082 `/scratch/stefan/7930160/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=CC=C1F) `REAL300000082996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082996 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 53, 60, 53, 53, 21, 6, 6, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 4, 1, 1, 53, 53, 53, 53, 53, 20, 6, 1, 4, 4, 4, 4, 1, 53, 53] 61 rigid atoms, others: [36, 8, 9, 10, 11, 12, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 37, 38]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082996 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 27, 27, 53, 53, 53, 61, 61, 53, 53, 61, 61, 61, 61, 61, 53, 53, 1, 1, 1, 1, 1, 9, 27, 53, 61, 61, 61, 61, 53, 1, 1] 61 rigid atoms, others: [1, 3, 4, 5, 6, 27, 24, 25, 26, 38, 28, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082996 none O=C([O-])C1=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 29, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 61, 61, 61, 61, 61, 29, 11, 4, 1, 1, 1, 1, 4, 61, 61] 61 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082996 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082996 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082996/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082996 Building REAL300000082997 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082997' /scratch/stefan/7930160/working/building/REAL300000082997 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082997 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082997/0 /scratch/stefan/7930160/working/building/REAL300000082997 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1083 `/scratch/stefan/7930160/working/3D/1083' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=C2)C=C1)C(=O)[O-]) `REAL300000082997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082997 none CC(OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [183, 121, 55, 40, 63, 63, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 183, 201, 201, 183, 183, 183, 182, 63, 63, 23, 6, 1, 1, 1, 63, 63] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 679 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: REAL300000082997 none CC(OC1=CC=C(C=NNC2=CC=C(F)C(C(=O)[O-])=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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [17, 6, 1, 1, 1, 1, 1, 1, 8, 8, 32, 63, 63, 63, 63, 63, 63, 100, 100, 63, 1, 1, 17, 26, 26, 17, 17, 17, 17, 1, 1, 8, 32, 63, 63, 63, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 36, 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]) total number of confs: 362 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082997 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082997 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082997/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082997 Building REAL300000082998 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082998' /scratch/stefan/7930160/working/building/REAL300000082998 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082998 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082998/0 /scratch/stefan/7930160/working/building/REAL300000082998 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1084 `/scratch/stefan/7930160/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=CC=C1F) `REAL300000082998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082998 none O=C([O-])C1=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 42, 43, 22, 23, 24, 25, 26, 27]) total number of confs: 38 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: REAL300000082998 none O=C([O-])C1=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 15, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082998 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082998 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082998/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082998 Building REAL300000082999 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000082999' /scratch/stefan/7930160/working/building/REAL300000082999 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000082999 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000082999/0 /scratch/stefan/7930160/working/building/REAL300000082999 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1085 `/scratch/stefan/7930160/working/3D/1085' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1) `REAL300000082999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000082999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000082999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082999 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 12, 12, 74, 151, 151, 151, 151, 151, 151, 160, 160, 151, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 74, 151, 151, 151, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 2, 37, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 437 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000082999 none CCC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 27, 151, 151, 151, 151, 151, 151, 54, 54, 54, 54, 54, 7, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 347 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000082999 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000082999 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000082999/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000082999 Building REAL300000083000 mkdir: created directory `/scratch/stefan/7930160/working/building/REAL300000083000' /scratch/stefan/7930160/working/building/REAL300000083000 /scratch/stefan/7930160/working /scratch/stefan/7930160 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000083000 mkdir: created directory `0' /scratch/stefan/7930160/working/building/REAL300000083000/0 /scratch/stefan/7930160/working/building/REAL300000083000 /scratch/stefan/7930160/working /scratch/stefan/7930160 Protomer 0 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7930160/working/3D/1086 `/scratch/stefan/7930160/working/3D/1086' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1) `REAL300000083000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000083000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7930160/working/building/REAL300000083000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000083000 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 47, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 11, 11, 11, 47, 92, 92, 92, 1, 1, 1, 4, 4, 1] 111 rigid atoms, others: [32, 1, 34, 37, 33, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 185 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000083000 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [37, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 92, 92, 92, 92, 92, 111, 111, 111, 111, 92, 38, 38, 38, 9, 1, 1, 1, 92, 92, 92, 111, 111, 92] 111 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000083000 none CC(=NNC1=CC=C(F)C(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [21, 4, 21, 21, 68, 111, 111, 111, 111, 111, 111, 111, 111, 111, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 68, 111, 111, 111, 4, 4, 4, 1, 1, 4] 111 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]) total number of confs: 238 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7930160/working/building/REAL300000083000 /scratch/stefan/7930160/working /scratch/stefan/7930160 Finished preparing REAL300000083000 Recording results /scratch/stefan/7930160/working /scratch/stefan/7930160 Appending to /scratch/stefan/7930160/finished/xaaaade.* 0: /scratch/stefan/7930160/working/building/REAL300000083000/0.* Removing working files in /scratch/stefan/7930160/working/building/REAL300000083000 /scratch/stefan/7930160 Compressing combined databse files /scratch/stefan/7930160/finished/xaaaade.db2.gz /scratch/stefan/7930160/finished/xaaaade.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7930160/finished) ======================================================= Finalizing... removed `/scratch/stefan/7930160/working/3D/1087' removed directory: `/scratch/stefan/7930160/working/3D' `/scratch/stefan/7930160/working/protonate' -> `/scratch/stefan/7930160/archive' `/scratch/stefan/7930160/working/input-smiles.ism' -> `/scratch/stefan/7930160/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7930160/working/building' rmdir: removing directory, `/scratch/stefan/7930160/working' ls: No match. ls: No match.